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Lyase PDB id
Protein chains
586 a.a. *
SO4 ×5
FMT ×4
Waters ×661
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme a decarboxylase
Structure: Glutaconyl-coa decarboxylase a subunit. Chain: a, b. Synonym: carboxyltransferase. Engineered: yes
Source: Acidaminococcus fermentans. Organism_taxid: 905. Gene: gcda. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
2.20Å     R-factor:   0.201     R-free:   0.227
Authors: K.S.Wendt,I.Schall,R.Huber,W.Buckel,U.Jacob
Key ref: K.S.Wendt et al. (2003). Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase. EMBO J, 22, 3493-3502. PubMed id: 12853465
30-May-03     Release date:   05-Aug-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q06700  (GCDA_ACIFV) -  Glutaconyl-CoA decarboxylase subunit alpha
587 a.a.
586 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Glutaconyl-CoA decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-carboxybut-2-enoyl-CoA = but-2-enoyl-CoA + CO2
= but-2-enoyl-CoA
Bound ligand (Het Group name = FMT)
corresponds exactly
      Cofactor: Biotin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transport   4 terms 
  Biochemical function     lyase activity     4 terms  


EMBO J 22:3493-3502 (2003)
PubMed id: 12853465  
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
K.S.Wendt, I.Schall, R.Huber, W.Buckel, U.Jacob.
Glutaconyl-CoA decarboxylase is a biotin-dependent ion pump whereby the free energy of the glutaconyl-CoA decarboxylation to crotonyl-CoA drives the electrogenic transport of sodium ions from the cytoplasm into the periplasm. Here we present the crystal structure of the decarboxylase subunit (Gcdalpha) from Acidaminococcus fermentans and its complex with glutaconyl-CoA. The active sites of the dimeric Gcdalpha lie at the two interfaces between the mono mers, whereas the N-terminal domain provides the glutaconyl-CoA-binding site and the C-terminal domain binds the biotinyllysine moiety. The Gcdalpha catalyses the transfer of carbon dioxide from glutaconyl-CoA to a biotin carrier (Gcdgamma) that subsequently is decarboxylated by the carboxybiotin decarboxylation site within the actual Na(+) pump (Gcdbeta). The analysis of the active site lead to a novel mechanism for the biotin-dependent carboxy transfer whereby biotin acts as general acid. Furthermore, we propose a holoenzyme assembly in which the water-filled central channel of the Gcdalpha dimer lies co-axial with the ion channel (Gcdbeta). The central channel is blocked by arginines against passage of sodium ions which might enter the central channel through two side channels.

Literature references that cite this PDB file's key reference

  PubMed id Reference
22158123 C.S.Huang, P.Ge, Z.H.Zhou, and L.Tong (2012).
An unanticipated architecture of the 750-kDa α6β6 holoenzyme of 3-methylcrotonyl-CoA carboxylase.
  Nature, 481, 219-223.
PDB codes: 3u9r 3u9s 3u9t
21204864 G.Gago, L.Diacovich, A.Arabolaza, S.C.Tsai, and H.Gramajo (2011).
Fatty acid biosynthesis in actinomycetes.
  FEMS Microbiol Rev, 35, 475-497.  
20725044 C.S.Huang, K.Sadre-Bazzaz, Y.Shen, B.Deng, Z.H.Zhou, and L.Tong (2010).
Crystal structure of the alpha(6)beta(6) holoenzyme of propionyl-coenzyme A carboxylase.
  Nature, 466, 1001-1005.
PDB code: 3n6r
19654317 D.Kress, D.Brügel, I.Schall, D.Linder, W.Buckel, and L.O.Essen (2009).
An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases.
  J Biol Chem, 284, 28401-28409.
PDB codes: 3gf3 3gf7 3glm 3gma
19369256 J.Bains, R.Leon, and M.J.Boulanger (2009).
Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400: A NOVEL RING-CLEAVING ENZYME IN THE CROTONASE SUPERFAMILY.
  J Biol Chem, 284, 16377-16385.
PDB code: 2w3p
19395484 S.Wischgoll, M.Taubert, F.Peters, N.Jehmlich, M.von Bergen, and M.Boll (2009).
Decarboxylating and nondecarboxylating glutaryl-coenzyme A dehydrogenases in the aromatic metabolism of obligately anaerobic bacteria.
  J Bacteriol, 191, 4401-4409.  
18039764 G.Herrmann, E.Jayamani, G.Mai, and W.Buckel (2008).
Energy conservation via electron-transferring flavoprotein in anaerobic bacteria.
  J Bacteriol, 190, 784-791.  
17298082 A.A.Hoskins, M.Morar, T.J.Kappock, I.I.Mathews, J.B.Zaugg, T.E.Barder, P.Peng, A.Okamoto, S.E.Ealick, and J.Stubbe (2007).
N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.
  Biochemistry, 46, 2842-2855.
PDB codes: 2ate 2nsh 2nsj 2nsl
  17277455 M.Yamada, R.Natsume, T.Nakamatsu, S.Horinouchi, H.Kawasaki, and T.Senda (2007).
Crystallization and preliminary crystallographic analysis of DtsR1, a carboxyltransferase subunit of acetyl-CoA carboxylase from Corynebacterium glutamicum.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 120-122.  
17478501 S.J.Suhrer, M.Gruber, and M.J.Sippl (2007).
QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.
  Nucleic Acids Res, 35, W411-W415.  
15647905 P.Dahinden, Y.Auchli, T.Granjon, M.Taralczak, M.Wild, and P.Dimroth (2005).
Oxaloacetate decarboxylase of Vibrio cholerae: purification, characterization, and expression of the genes in Escherichia coli.
  Arch Microbiol, 183, 121-129.  
  15374661 J.Kim, M.Hetzel, C.D.Boiangiu, and W.Buckel (2004).
Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of alpha-amino acids by anaerobic bacteria.
  FEMS Microbiol Rev, 28, 455-468.  
15490124 P.Dahinden, K.M.Pos, M.Taralczak, and P.Dimroth (2004).
Oxaloacetate decarboxylase of Archaeoglobus fulgidus: cloning of genes and expression in Escherichia coli.
  Arch Microbiol, 182, 414-420.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.