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(-) Description

Title :  MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LYSA)
 
Authors :  K. Gokulan, B. Rupp, M. S. Pavelka Jr, W. R. Jacobs Jr, J. C. Sacchettin Structural Genomics Consortium (Tbsgc)
Date :  11 Mar 03  (Deposition) - 20 Mar 03  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Decarboxylase, Diaminopimelate, Dapdc, Plp, Lysine Pathway, Mycbacterium Tuberculosis, Lysine Synthetic Pathway, Pyridoxal Phosphate, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tb, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Gokulan, B. Rupp, M. Pavelka, W. Jacobs, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis Diaminopimelate Decarboxylase, An Essential Enzyme In Bacterial Lysine Biosynthesis
J. Biol. Chem. V. 278 18588 2003
PubMed-ID: 12637582  |  Reference-DOI: 10.1074/JBC.M301549200

(-) Compounds

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834(DE3) MET-
    Expression System Taxid: 562
    Expression System Vector: PET30B/HIS
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Other Details: COMPLEXED WITH COFACTOR PLP AND PRODUCT LYSINE
    Other Details - Source: C-TERM 6-HIS TAG
    Strain: H37RV
    Synonym: DAP DECARBOXYLASE, MESO-DIAMINOPIMELATE DECARBOXYLASE, LYSA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1LYS2Mod. Amino AcidLYSINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:72 , SER A:216 , ARG A:303 , ARG A:344 , GLU B:376BINDING SITE FOR RESIDUE LYS A 501
2AC2SOFTWAREGLU A:376 , SER A:377 , TYR A:413 , LYS B:72 , HIS B:213 , SER B:216 , ARG B:303 , TYR B:348 , TYR B:405BINDING SITE FOR RESIDUE LYS B 501
3AC3SOFTWAREALA A:70 , LYS A:72 , ARG A:161 , HIS A:213 , GLY A:257 , GLY A:258 , GLU A:300 , GLY A:302 , ARG A:303 , TYR A:405 , HOH A:2064 , HOH A:2109 , CYS B:375BINDING SITE FOR RESIDUE PLP A 500
4AC4SOFTWARECYS A:375 , LYS B:72 , HIS B:213 , SER B:216 , GLY B:257 , GLY B:258 , GLU B:300 , GLY B:302 , ARG B:303 , TYR B:405 , HOH B:2126 , HOH B:2127BINDING SITE FOR RESIDUE PLP B 500

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:93 -B:375
2A:375 -B:93

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:40 -Pro A:41
2Thr B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HKV)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_MYCBO69-87
 		  2A:69-87
B:69-87
DCDA_MYCTO69-87
 		  2A:69-87
B:69-87
DCDA_MYCTU69-87
 		  2A:69-87
B:69-87
2ODR_DC_2_2PS00879 Orn/DAP/Arg decarboxylases family 2 signature 2.DCDA_MYCBO243-260
 		  2A:243-260
B:243-260
DCDA_MYCTO243-260
 		  2A:243-260
B:243-260
DCDA_MYCTU243-260
 		  2A:243-260
B:243-260

(-) Exons   (0, 0)

(no "Exon" information available for 1HKV)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCBO | P0A5M5 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCBO     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkva1 A:2-45,A:311-447                    d1hkva2 A:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkva1 A:2-45,A:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvA01 A:2-46,A:308-447                     1hkvA02 A:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvA01 A:2-46,A:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhh..eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeee......hhhhh.hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv A   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501


Chain A from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCTO | P9WIU6 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCTO     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkva1 A:2-45,A:311-447                    d1hkva2 A:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkva1 A:2-45,A:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvA01 A:2-46,A:308-447                     1hkvA02 A:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvA01 A:2-46,A:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhh..eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeee......hhhhh.hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv A   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501


Chain A from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCTU | P9WIU7 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCTU     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkva1 A:2-45,A:311-447                    d1hkva2 A:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkva1 A:2-45,A:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvA01 A:2-46,A:308-447                     1hkvA02 A:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvA01 A:2-46,A:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhh..eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeee......hhhhh.hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------ODR_DC_2_1         -----------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv A   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501


Chain B from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCBO | P0A5M5 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCBO     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkvb1 B:2-45,B:311-447                    d1hkvb2 B:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkvb1 B:2-45,B:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvB01 B:2-46,B:308-447                     1hkvB02 B:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvB01 B:2-46,B:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeeee...........hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv B   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501


Chain B from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCTO | P9WIU6 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCTO     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkvb1 B:2-45,B:311-447                    d1hkvb2 B:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkvb1 B:2-45,B:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvB01 B:2-46,B:308-447                     1hkvB02 B:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvB01 B:2-46,B:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeeee...........hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv B   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501


Chain B from PDB  Type:PROTEIN  Length:447
 aligned with DCDA_MYCTU | P9WIU7 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     | 
           DCDA_MYCTU     2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVR-   -
               SCOP domains d1hkvb1 B:2-45,B:311-447                    d1hkvb2 B:46-310 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                      d1hkvb1 B:2-45,B:311-447 Diaminopimelate decarboxylase LysA                                                                              - SCOP domains
               CATH domains 1hkvB01 B:2-46,B:308-447                     1hkvB02 B:47-307 Alanine racemase                                                                                                                                                                                                                                    1hkvB01 B:2-46,B:308-447 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee.....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhh.hhhh.eee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeeeee..eeeee.eeee.........ee...hhhhhhhhhhhhh..eeeeeee...eeee..hhhhhhhhhhhhhhhhhhhhhhh........eee................hhhhhhhhhhhhhhhhhhh......eee...hhhhhh..eeeeee..eeeeee.....eeeeee........hhhhhhh....eee........eeeeeee........eeeeeeeee.......eeeee...........hhhhh...eeeeee..eeeeee...hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------ODR_DC_2_1         -----------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2        -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hkv B   2 NELLHLAPNVWPRNTTRDEVGVVCIAGIPLTQLAQEYGTPLFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVALHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVRLTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDVDGFELAAHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAELAAKLGTIVSDESTAVGLPTPKLVVEPGRAIAGPGTITLYEVGTVKDVDVSATAHRRYVSVDGGMSDNIRTALYGAQYDVRLVSRVSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRPAVVAVHAGNARLVLRRETVDDLLSLEVRK 501
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       447|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        501
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HKV)

(-) Gene Ontology  (11, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DCDA_MYCBO | P0A5M5)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008836    diaminopimelate decarboxylase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Chain A,B   (DCDA_MYCTO | P9WIU6)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008836    diaminopimelate decarboxylase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Chain A,B   (DCDA_MYCTU | P9WIU7)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008836    diaminopimelate decarboxylase activity    Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DCDA_MYCBO | P0A5M5: 1hkw
        DCDA_MYCTO | P9WIU6: 1hkw 2o0t
        DCDA_MYCTU | P9WIU7: 1hkw 2o0t

(-) Related Entries Specified in the PDB File

1hkw MYCOBACTERIUM DIAMINOPIMELATE DICARBOXYLASE (LYSA) RELATED ID: RV1293 RELATED DB: TARGETDB