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(-) Description

Title :  CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE
 
Authors :  V. Levdikov, L. Blagova, N. Bose, C. Momany
Date :  19 Dec 01  (Deposition) - 11 Nov 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pyridoxal-Phosphate, Decarboxylation, Diaminopimelate, Lysine, Tim- Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Levdikov, L. Blagova, N. Bose, C. Momany
Diaminopimelate Decarboxylase Uses A Versatile Active Site For Stereospecific Decarboxylation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LYSA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DAP DECARBOXYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1LI2Ligand/IonLITHIUM ION
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1LI-1Ligand/IonLITHIUM ION
2MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
4SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMES A:510 , HOH A:704 , HOH A:784BINDING SITE FOR RESIDUE SO4 A 520
2AC2SOFTWAREHIS A:151 , SER A:152 , LYS A:154 , ASN A:156 , HOH A:645BINDING SITE FOR RESIDUE LI A 530
3AC3SOFTWAREASN A:303 , SER A:384 , ARG A:389 , PRO A:390 , LEU A:391 , HOH A:590BINDING SITE FOR RESIDUE LI A 540
4AC4SOFTWAREALA A:52 , LYS A:54 , THR A:100 , HIS A:191 , GLY A:227 , GLU A:268 , GLY A:270 , ARG A:271 , CYS A:342 , TYR A:378 , MES A:510 , HOH A:595 , HOH A:602 , HOH A:614 , HOH A:629 , HOH A:631BINDING SITE FOR RESIDUE PLP A 554
5AC5SOFTWARELYS A:54 , THR A:157 , HIS A:191 , TYR A:311 , GLU A:343 , SER A:344 , TYR A:378 , SO4 A:520 , PLP A:554 , HOH A:609 , HOH A:614 , HOH A:704 , HOH A:864BINDING SITE FOR RESIDUE MES A 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KNW)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Cys A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_ECOLI51-69  1A:51-69
2ODR_DC_2_2PS00879 Orn/DAP/Arg decarboxylases family 2 signature 2.DCDA_ECOLI216-229  1A:216-229
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ODR_DC_2_1PS00878 Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.DCDA_ECOLI51-69  2A:51-69
2ODR_DC_2_2PS00879 Orn/DAP/Arg decarboxylases family 2 signature 2.DCDA_ECOLI216-229  2A:216-229

(-) Exons   (0, 0)

(no "Exon" information available for 1KNW)

(-) 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:421
 aligned with DCDA_ECOLI | P00861 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                            420  
                                    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        |- 
           DCDA_ECOLI     2 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELL--   -
               SCOP domains d1knwa1 A:2-31,A:279-422      d1knwa2 A:32-278 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                    d1knwa1 A:2-31,A:279-422 Diaminopimelate decarboxylase LysA                                                                                      SCOP domains
               CATH domains 1knwA01 A:2-32,A:278-422       1knwA02 A:33-277 Alanine racemase                                                                                                                                                                                                                    1knwA01 A:2-32,A:278-422 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                        CATH domains
               Pfam domains ------------------------------Orn_Arg_deC_N-1knwA01 A:32-276                                                                                                                                                                                                                       --Orn_DAP_Arg_deC-1knwA02 A:279-397                                                                                      ------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh..eeeeehhhhhhhhhh.....eeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..........eeeee...hhhhhhhhhhhh..eee.hhhhhhhhhhhh...eeeeeee.....................ee..hhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhhhh....eee................hhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhh..eeeeeeeeeeeee..eeeeee.......hhhhhhh....eeee...........eeeeeee....................eeee......eeee......hhhhh..........eeeee..eeeeee...hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------ODR_DC_2_1         --------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knw A   2 PHSLFSTDTDLTAENLLRLPAEFGCPVWVYDAQIIRRQIAALKQFDVVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSGVLITQVRSVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHISALAADGRSLEHAPTVETVVAGPLCESGDVFTQQEGGNVETRALPEVKAGDYLVLHDTGAYGASMSSNYNSRPLLPEVLFDNGQARLIRRRQTIEELLALELLHH 422
                                    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
   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, 2)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: Orn_DAP_Arg_deC] (18)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCDA_ECOLI | P00861)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        DCDA_ECOLI | P00861: 1ko0

(-) Related Entries Specified in the PDB File

1ko0 CRYSTAL STRUCTURE OF A D,L-LYSINE COMPLEX OF DIAMINOPIMELATE DECARBOXYLASE