4HL6

YfdE from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Function and X-Ray crystal structure of Escherichia coli YfdE.

Mullins, E.A.Sullivan, K.L.Kappock, T.J.

(2013) Plos One 8: e67901-e67901

  • DOI: 10.1371/journal.pone.0067901

  • PubMed Abstract: 
  • Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxa ...

    Many food plants accumulate oxalate, which humans absorb but do not metabolize, leading to the formation of urinary stones. The commensal bacterium Oxalobacter formigenes consumes oxalate by converting it to oxalyl-CoA, which is decarboxylated by oxalyl-CoA decarboxylase (OXC). OXC and the class III CoA-transferase formyl-CoA:oxalate CoA-transferase (FCOCT) are widespread among bacteria, including many that have no apparent ability to degrade or to resist external oxalate. The EvgA acid response regulator activates transcription of the Escherichia coli yfdXWUVE operon encoding YfdW (FCOCT), YfdU (OXC), and YfdE, a class III CoA-transferase that is ~30% identical to YfdW. YfdW and YfdU are necessary and sufficient for oxalate-induced protection against a subsequent acid challenge; neither of the other genes has a known function. We report the purification, in vitro characterization, 2.1-Å crystal structure, and functional assignment of YfdE. YfdE and UctC, an orthologue from the obligate aerobe Acetobacter aceti, perform the reversible conversion of acetyl-CoA and oxalate to oxalyl-CoA and acetate. The annotation of YfdE as acetyl-CoA:oxalate CoA-transferase (ACOCT) expands the scope of metabolic pathways linked to oxalate catabolism and the oxalate-induced acid tolerance response. FCOCT and ACOCT active sites contain distinctive, conserved active site loops (the glycine-rich loop and the GNxH loop, respectively) that appear to encode substrate specificity.


    Organizational Affiliation

    Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein YfdE
A, B, C, D, E, F
401Escherichia coli (strain K12)Gene Names: yfdE
EC: 2.8.3.19
Find proteins for P76518 (Escherichia coli (strain K12))
Go to UniProtKB:  P76518
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/272 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 111.422α = 90.00
b = 79.527β = 99.95
c = 276.189γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
SCALEPACKdata scaling
HKL-2000data reduction
DENZOdata reduction
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2013-08-21
    Type: Database references
  • Version 1.3: 2014-03-26
    Type: Structure summary
  • Version 1.4: 2017-11-15
    Type: Refinement description