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(-) Description

Title :  GLUTACONYL-COA DECARBOXYLASE A SUBUNIT FROM CLOSTRIDIUM SYMBIOSUM CO-CRYSTALLIZED WITH GLUTARYL-COA
 
Authors :  D. Kress, D. Brugel, W. Buckel, L. -O. Essen
Date :  13 Mar 09  (Deposition) - 28 Jul 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GRA2Ligand/IonGLUTARYL-COENZYME A
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1GRA4Ligand/IonGLUTARYL-COENZYME A

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:50 , THR A:51 , MET A:118 , SER A:151 , GLY A:152 , VAL A:153 , GLU A:154 , PHE A:155 , THR A:192 , PRO A:194 , ALA A:195 , GLY A:196 , ALA A:459 , ALA A:460 , VAL A:487 , MET A:497 , ARG A:500 , LYS A:501 , HOH A:747BINDING SITE FOR RESIDUE GRA A 589
2AC2SOFTWAREMET B:118 , SER B:151 , GLY B:152 , VAL B:153 , GLU B:154 , PHE B:155 , ALA B:195 , GLY B:196 , ALA B:459 , ALA B:460 , VAL B:487 , ARG B:500 , HOH B:732BINDING SITE FOR RESIDUE GRA B 589

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:375 -Pro A:376
2Ala B:220 -Gly B:221
3Tyr B:375 -Pro B:376

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GMA)

(-) 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:558
 aligned with B7TVP1_CLOSY | B7TVP1 from UniProtKB/TrEMBL  Length:588

    Alignment length:584
                                    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 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAGILSGMNPKGYIDDEAAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAKKAGEDLQPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETF 586
               SCOP domains d3gmaa1 A:3-291 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                           d3gmaa2 A:292-586 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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....---------------hhhhhhhhhhhhhhhh.....hhhhhh.......eee.hhhhhhhhhhhhhhhh...hhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhh.ee........eeeeeeee..eeeeeeee...ee...........ee..eehhhhhhhhhhhhhhhhhh...eeeee...ee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eee.hhhhhh........eeeeee....eee..hhhhhhhhhhh..-----------hhhhhhhhhhhhhhhhh.hhhhhhhh....ee.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gma A   3 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGA---------------AAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRK-----------QPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETF 586
                                    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        |-         -|      522       532       542       552       562       572       582    
                                                                                                                                                                                                                                                   220             236                                                                                                                                                                                                                                                                      501         513                                                                         


Chain B from PDB  Type:PROTEIN  Length:566
 aligned with B7TVP1_CLOSY | B7TVP1 from UniProtKB/TrEMBL  Length:588

    Alignment length:584
                                    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 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAGILSGMNPKGYIDDEAAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKAKKAGEDLQPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETF 586
               SCOP domains d3gmab1 B:3-291 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                           d3gmab2 B:292-586 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.....-----------hhhhhhhhhhhhhhhhhhh.....hhhhhh.......eee.hhhhhhhhhhhhhhhh...hhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhh.ee........eeeeeeee..eeeeeeee...eee.........eee..eehhhhhhhhhhhhhhhhhh...eeeee...ee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eee.hhhhhh........eeeeee....eee..hhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhh.hhhhhhhh....ee.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gma B   3 MYSMPGYFQNMPTIGKELVNPNPENEQEIKAVESDIHESIKKALDAGITSEEKLNERGQLSAMQRINALIDPGTWCPLNSLFNPENNKFGTTNIVNGLGRVDGKWVYIVASDNKKMAGAWVPGQAENLIRCSDAAKMMHLPLIYLLNCSGVEFPNQDKVYPNRRGGGTPFFRNSELNQLGIPVIVGIYGTNPAGGGYHSISPTILIAHQDANMAVGGAG-----------DDEAAEQIIAAQIENSKLKVPAPGSVPIHYDETGFFREVYQNDLGVIDGIKKYISYLPAYNLEFFRVDTPKAPQLPAEDLYSIIPMNQKRPYDIYEVIARLFDNSEFSEYKKGYGPEMVTGLAKVNGLLVGVIANVQGLLMNYPEYKQNSVGIGGKLYRQGLIKMNEFVTLCARDRIPLIWLQDTTGIDVGDEAEKAELLGLGQSLIYSIENSKLPSLEITIRKASAAAHYVLGGPQGNNTNVFSIGTGACEYYVMPGETAANAMYSRKLVKA-------QPIIGKMNDMIQMYTDKSRPKYCTEKGMVDEIVDMTEVRPYIQAFTEAAYQNPQSICPMHQMLTPRSTREFETF 586
                                    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         233                                                                                                                                                                                                                                                                             505     513
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GMA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

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

UniProtKB/TrEMBL
        B7TVP1_CLOSY | B7TVP1: 3gf3 3gf7 3glm

(-) Related Entries Specified in the PDB File

3gf3 GLUTACONYL-COA DECARBOXYLASE A SUBUNIT FROM CLOSTRIDIUM SYMBIOSUM CO-CRYSTALLIZED WITH GLUTACONYL-COA
3gf7 GLUTACONYL-COA DECARBOXYLASE A SUBUNIT FROM CLOSTRIDIUM SYMBIOSUM APOPROTEIN
3glm GLUTACONYL-COA DECARBOXYLASE A SUBUNIT FROM CLOSTRIDIUM SYMBIOSUM CO-CRYSTALLIZED WITH CROTONYL-COA