3GLM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M109.037762
  • Primary Citation of Related Structures:  

  • 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 membr ...

    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

    Biochemie, Fachbereich Chemie, Philipps-Universit├Ąt Marburg, D-35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutaconyl-CoA decarboxylase subunit A
A, B, C, D
588Clostridium symbiosumMutation(s): 0 
Gene Names: gcdA
EC: 4.1.1.70
Find proteins for B7TVP1 (Clostridium symbiosum)
Go to UniProtKB:  B7TVP1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
COO
Query on COO

Download SDF File 
Download CCD File 
A, B, C, D
CROTONYL COENZYME A
C25 H40 N7 O17 P3 S
KFWWCMJSYSSPSK-XBTRWLRFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.500α = 90.00
b = 167.450β = 89.98
c = 138.110γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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