1PT8

Crystal structure of the yfdW gene product of E. coli, in complex with oxalate and acetyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history


Literature

The crystal structure of the Escherichia coli yfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases.

Gruez, A.Roig-Zamboni, V.Valencia, C.Campanacci, V.Cambillau, C.

(2003) J Biol Chem 278: 34582-34586

  • DOI: https://doi.org/10.1074/jbc.C300282200
  • Primary Citation of Related Structures:  
    1PT5, 1PT7, 1PT8

  • PubMed Abstract: 

    Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.


  • Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille, Cedex 20, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hypothetical protein yfdW
A, B
437Escherichia coliShigella flexneri
This entity is chimeric
Mutation(s): 0 
Gene Names: YFDW OR B2374 OR SF2441
UniProt
Find proteins for P69902 (Escherichia coli (strain K12))
Explore P69902 
Go to UniProtKB:  P69902
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69902
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.786α = 90
b = 146.786β = 90
c = 129.905γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance