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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF DIAMINOPIMELATE DECARBOXYLATE (LYSA)
 
Authors :  Y. Nakamura, Y. Bessho, B. Padmanabhan, S. Yokoyama, Riken Structura Genomics/Proteomics Initiative (Rsgi)
Date :  27 Apr 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Tm1517, Tim Beta/Alpha Barrel Fold, Lyase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nakamura, Y. Bessho, B. Padmanabhan, S. Yokoyama
Crystal Structure Analysis Of Diaminopimelate Decarboxylate (Lysa)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System StrainROSETTA834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid243274
    StrainMSB8
    SynonymLYSA, DAP DECARBOXYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 22)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:46 , ASP A:65 , HIS A:179 , SER A:182 , GLY A:214 , GLU A:246 , GLY A:248 , ARG A:249 , CYS A:314 , TYR A:343 , HOH A:404 , HOH A:450 , HOH A:612BINDING SITE FOR RESIDUE PLP A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YXX)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YXX)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_THEMA43-61  1A:43-61
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_THEMA43-61  1A:43-61
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_THEMA43-61  2A:43-61

(-) Exons   (0, 0)

(no "Exon" information available for 2YXX)

(-) Sequences/Alignments

Asymmetric 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:385
 aligned with DCDA_THEMA | Q9X1K5 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:385
                                    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     
           DCDA_THEMA     2 DILRKVAEIHGTPTYVYFEETLRKRSRLVKEVFEGVNLLPTFAVKANNNPVLLKILREEGFGMDVVTKGELLAAKLAGVPSHTVVWNGNGKSRDQMEHFLREDVRIVNVDSFEEMEIWRELNPEGVEYFIRVNPEVDAKTHPHISTGLKKHKFGIPLEDLDSFMERFRSMNIRGLHVHIGSQITRVEPFVEAFSKVVRASERYGFEEINIGGGWGINYSGEELDLSSYREKVVPDLKRFKRVIVEIGRYIVAPSGYLLLRVVLVKRRHNKAFVVVDGGMNVLIRPALYSAYHRIFVLGKQGKEMRADVVGPLCESGDVIAYDRELPEVEPGDIIAVENAGAYGYTMSNNYNSTTRPAEVLVRENGRISLIRRRETEMDIFKDVVM 386
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------Orn_Arg_deC_N-2yxxA01 A:20-254                                                                                                                                                                                                             --Orn_DAP_Arg_deC-2yxxA02 A:257-362                                                                         ------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..eeeeehhhhhhhhhhhhhhh....eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhh...ee..hhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhh..eee..............hhhhhhhhhhhhhh...eeeeeehhhhhh..eeeeeeeeeeeee..eeeeee.......hhhhhh.....eee.......eeeeee........eeeeeeee.......eeee......hhhhh.........eeeee.....eeeee...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yxx A   2 DILRKVAEIHGTPTYVYFEETLRKRSRLVKEVFEGVNLLPTFAVKANNNPVLLKILREEGFGmDVVTKGELLAAKLAGVPSHTVVWNGNGKSRDQmEHFLREDVRIVNVDSFEEmEIWRELNPEGVEYFIRVNPEVDAKTHPHISTGLKKHKFGIPLEDLDSFmERFRSmNIRGLHVHIGSQITRVEPFVEAFSKVVRASERYGFEEINIGGGWGINYSGEELDLSSYREKVVPDLKRFKRVIVEIGRYIVAPSGYLLLRVVLVKRRHNKAFVVVDGGmNVLIRPALYSAYHRIFVLGKQGKEmRADVVGPLCESGDVIAYDRELPEVEPGDIIAVENAGAYGYTmSNNYNSTTRPAEVLVRENGRISLIRRRETEmDIFKDVVm 386
                                    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    |
                                                                                         64-MSE                           97-MSE            116-MSE                                          165-MSE |                                                                                                          280-MSE                  305-MSE                                   347-MSE                        378-MSE 386-MSE
                                                                                                                                                                                                   171-MSE                                                                                                                                                                                                                   

   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2YXX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YXX)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCDA_THEMA | Q9X1K5)
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.

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