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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF 2,2-DIALKYLGLYCINE DECARBOXYLASE WITH DCS
 
Authors :  V. N. Malashkevich, M. D. Toney, P. Strop, J. Keller, J. N. Jansonius
Date :  19 Oct 99  (Deposition) - 19 Nov 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Enzyme Complexes, Catalytic Mechanism, Decarboxylation Inhibitor, Lysase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. N. Malashkevich, P. Strop, J. W. Keller, J. N. Jansonius, M. D. Toney
Crystal Structures Of Dialkylglycine Decarboxylase Inhibito Complexes.
J. Mol. Biol. V. 294 193 1999
PubMed-ID: 10556038  |  Reference-DOI: 10.1006/JMBI.1999.3254
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE))
    ChainsA
    EC Number4.1.1.64
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKDHE19
    Expression System StrainTY103
    Expression System Taxid562
    Organism ScientificBURKHOLDERIA CEPACIA
    Organism Taxid292
    SynonymDGD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1DCS1Ligand/IonD-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
2K1Ligand/IonPOTASSIUM ION
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1DCS4Ligand/IonD-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE
2K-1Ligand/IonPOTASSIUM ION
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:95 , THR A:98 , PRO A:99 , LEU A:102BINDING SITE FOR RESIDUE NA A 435
2AC2SOFTWARELEU A:78 , SER A:80 , THR A:303 , VAL A:305 , ASP A:307 , HOH A:529BINDING SITE FOR RESIDUE K A 436
3AC3SOFTWAREGLN A:52 , GLY A:111 , ALA A:112 , ASN A:115 , TRP A:138 , HIS A:139 , GLU A:210 , SER A:215 , ASP A:243 , ALA A:245 , GLN A:246 , LYS A:272 , TYR A:301 , THR A:302 , THR A:303 , ARG A:406 , HOH A:504 , HOH A:511 , HOH A:513 , HOH A:602 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE DCS A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1D7S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1D7S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D7S)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.DGDA_BURCE240-277  1A:240-277
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.DGDA_BURCE240-277  4A:240-277

(-) Exons   (0, 0)

(no "Exon" information available for 1D7S)

(-) 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:431
 aligned with DGDA_BURCE | P16932 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:431
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432 
           DGDA_BURCE     3 LNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSGMLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 433
               SCOP domains d1d7sa_ A: Dialkylglycine decarboxylase                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------1d7sA01 A:29-60,A:325-433       1d7sA02 A:61-324 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                    1d7sA01 A:29-60,A:325-433 Aspartate Aminotransferase, domain 1                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh...............eeee................hhhhhhhhhhhhhhhhh...eeeeee..ee.....ee...hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh....eeeeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhhhhhhhhhhhee..ee......eeeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:240-277   ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d7s A   3 LNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSGMLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAAVGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVVQRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 433
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432 

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1D7S)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (DGDA_BURCE | P16932)
molecular function
    GO:0047432    2,2-dialkylglycine decarboxylase (pyruvate) activity    Catalysis of the reaction: 2,2-dialkylglycine + H(+) + pyruvate = L-alanine + CO(2) + dialkyl ketone.
    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: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.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DGDA_BURCE | P169321d7r 1d7u 1d7v 1dgd 1dge 1dka 1m0n 1m0o 1m0p 1m0q 1z3z 1zc9 1zob 1zod 2dkb

(-) Related Entries Specified in the PDB File

1d7r 1d7u 1d7v