Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum co-crystallized with crotonyl-coA

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases

Kress, D.Brugel, D.Schall, I.Linder, D.Buckel, W.Essen, L.-O.

(2009) J Biol Chem 284: 28401-28409

  • DOI: https://doi.org/10.1074/jbc.M109.037762
  • Primary Citation of Related Structures:  
    3GF3, 3GF7, 3GLM, 3GMA

  • PubMed Abstract: 

    Glutaconyl-CoA decarboxylase (Gcd) couples the biotin-dependent decarboxylation of glutaconyl-CoA with the generation of an electrochemical Na(+) gradient. Sequencing of the genes encoding all subunits of the Clostridium symbiosum decarboxylase membrane complex revealed that it comprises two distinct biotin carrier subunits, GcdC(1) and GcdC(2), which differ in the length of a central alanine- and proline-rich linker domain. Co-crystallization of the decarboxylase subunit GcdA with the substrate glutaconyl-CoA, the product crotonyl-CoA, and the substrate analogue glutaryl-CoA, respectively, resulted in a high resolution model for substrate binding and catalysis revealing remarkable structural changes upon substrate binding. Unlike the GcdA structure from Acidaminococcus fermentans, these data suggest that in intact Gcd complexes, GcdA is associated as a tetramer crisscrossed by a network of solvent-filled tunnels.

  • Organizational Affiliation

    Mikrobiologie, Fachbereich Biologie, Philipps-Universität Marburg, D-35032 Marburg, Germany; Max-Plank-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany. Electronic address: buckel@staff.uni-marburg.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutaconyl-CoA decarboxylase subunit A
A, B, C, D
588[Clostridium] symbiosumMutation(s): 0 
Gene Names: gcdADXA34_11530ERS852479_00963
Find proteins for B7TVP1 (Clostridium symbiosum)
Explore B7TVP1 
Go to UniProtKB:  B7TVP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7TVP1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.5α = 90
b = 167.45β = 89.98
c = 138.11γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Database references