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(-) Description

Title :  GLUTACONYL-COA DECARBOXYLASE A SUBUNIT FROM CLOSTRIDIUM SYMBIOSUM CO-CRYSTALLIZED WITH GLUTACONYL-COA
 
Authors :  D. Kress, D. Brugel, W. Buckel, L. -O. Essen
Date :  26 Feb 09  (Deposition) - 28 Jul 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Glutaconyl-Coa Decarboxylase, Sodium Ion Transport, Biotin, Glutamate Fermentation, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kress, D. Brugel, I. Schall, D. Linder, W. Buckel, L. -O. Essen
An Asymmetric Model For Na+-Translocating Glutaconyl-Coa Decarboxylases
J. Biol. Chem. V. 284 28401 2009
PubMed-ID: 19654317  |  Reference-DOI: 10.1074/JBC.M109.037762

(-) Compounds

Molecule 1 - GLUTACONYL-COA DECARBOXYLASE SUBUNIT A
    Chains: A
    EC Number: 4.1.1.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PASK-IBA7PLUS
    Expression System Strain: ROSETTA (DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GCDA
    Organism Scientific: CLOSTRIDIUM SYMBIOSUM
    Organism Taxid: 1512
    Strain: HB25

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2COO1Ligand/IonCROTONYL COENZYME A
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2COO4Ligand/IonCROTONYL COENZYME A

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:50 , ARG A:59 , MET A:118 , SER A:151 , GLY A:152 , VAL A:153 , GLU A:154 , PHE A:155 , ALA A:195 , GLY A:196 , ALA A:460 , TYR A:463 , VAL A:487 , MET A:488 , MET A:497 , ARG A:500 , LYS A:501 , HOH A:823 , HOH A:842 , HOH A:849 , HOH A:855 , HOH A:921BINDING SITE FOR RESIDUE COO A 589
2AC2SOFTWAREILE A:420 , ALA A:459 , ALA A:460 , ALA A:461 , HOH A:672BINDING SITE FOR RESIDUE CL A 590

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GF3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:375 -Pro A:376

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GF3)

(-) Exons   (0, 0)

(no "Exon" information available for 3GF3)

(-) 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:563
 aligned with B7TVP1_CLOSY | B7TVP1 from UniProtKB/TrEMBL  Length:588

    Alignment length:585
                                    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       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     
         B7TVP1_CLOSY     3 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAGILSGMNPKGYIDDEAAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAKKAGEDLQPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETFG 587
               SCOP domains d3gf3a1 A:3-291 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                           d3gf3a2 A:292-587 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3gf3A01 A:3-60 Single Helix bin                           3gf3A02 A:61-291 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                              3gf3A03 A:292-587 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhh.....eee...............eeeeeeee..eeeeeeee...hhhhh...hhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhh......hhhhhhhhhhhhh...eeeee..eeehhhhhhhhh..eeeee...eee.....---------------hhhhhhhhhhhhhh......hhhhhh.......eee.hhhhhhhhhhhhhhh....hhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhh.ee........eeeeeeee..eeeeeeee...eee.........eee..eehhhhhhhhhhhhhhhhhh...eeeee...ee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eee.hhhhhh........eeeeee....eee..hhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhh.hhhhhhhh....ee.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gf3 A   3 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAG---------------AEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKA-------QPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETFG 587
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        |-         -    |  242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  |      -|      522       532       542       552       562       572       582     
                                                                                                                                                                                                                                                    221             237                                                                                                                                                                                                                                                                         505     513
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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, 2)

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

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GF3)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (B7TVP1_CLOSY | B7TVP1)
molecular function
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

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 Related Entries

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UniProtKB/TrEMBL
        B7TVP1_CLOSY | B7TVP1: 3gf7 3glm 3gma

(-) Related Entries Specified in the PDB File

3gf7 3glm 3gma