1T4C

Formyl-CoA Transferase in complex with Oxalyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes

Jonsson, S.Ricagno, S.Lindqvist, Y.Richards, N.G.

(2004) J.Biol.Chem. 279: 36003-36012

  • DOI: 10.1074/jbc.M404873200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antipo ...

    Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antiporter. Formyl-CoA transferase is a critical enzyme in oxalate-dependent ATP synthesis and is the first Class III CoA-transferase for which a high resolution, three-dimensional structure has been determined (Ricagno, S., Jonsson, S., Richards, N., and Lindqvist, Y. (2003) EMBO J. 22, 3210-3219). We now report the first detailed kinetic characterizations of recombinant, wild type formyl-CoA transferase and a number of site-specific mutants, which suggest that catalysis proceeds via a series of anhydride intermediates. Further evidence for this mechanistic proposal is provided by the x-ray crystallographic observation of an acylenzyme intermediate that is formed when formyl-CoA transferase is incubated with oxalyl-CoA. The catalytic mechanism of formyl-CoA transferase is therefore established and is almost certainly employed by all other members of the Class III CoA-transferase family.


    Organizational Affiliation

    Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formyl-coenzyme A transferase
A
427Oxalobacter formigenesMutation(s): 0 
Gene Names: frc
EC: 2.8.3.16
Find proteins for O06644 (Oxalobacter formigenes)
Go to UniProtKB:  O06644
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Formyl-coenzyme A transferase
B
427Oxalobacter formigenesMutation(s): 0 
Gene Names: frc
EC: 2.8.3.16
Find proteins for O06644 (Oxalobacter formigenes)
Go to UniProtKB:  O06644
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OXX
Query on OXX
B
L-PEPTIDE LINKINGC6 H6 N O7ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.163α = 90.00
b = 100.163β = 90.00
c = 196.872γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2018-08-08
    Type: Advisory, Data collection, Source and taxonomy