5C4I

Structure of an Oxalate Oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.274 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Structure of an Oxalate Oxidoreductase Provides Insight into Microbial 2-Oxoacid Metabolism.

Gibson, M.I.Brignole, E.J.Pierce, E.Can, M.Ragsdale, S.W.Drennan, C.L.

(2015) Biochemistry 54: 4112-4120

  • DOI: 10.1021/acs.biochem.5b00521

  • PubMed Abstract: 
  • Thiamine pyrophosphate (TPP), a derivative of vitamin B1, is a versatile and ubiquitous cofactor. When coupled with [4Fe-4S] clusters in microbial 2-oxoacid:ferredoxin oxidoreductases (OFORs), TPP is involved in catalyzing low-potential redox reactio ...

    Thiamine pyrophosphate (TPP), a derivative of vitamin B1, is a versatile and ubiquitous cofactor. When coupled with [4Fe-4S] clusters in microbial 2-oxoacid:ferredoxin oxidoreductases (OFORs), TPP is involved in catalyzing low-potential redox reactions that are important for the synthesis of key metabolites and the reduction of N2, H(+), and CO2. We have determined the high-resolution (2.27 √Ö) crystal structure of the TPP-dependent oxalate oxidoreductase (OOR), an enzyme that allows microbes to grow on oxalate, a widely occurring dicarboxylic acid that is found in soil and freshwater and is responsible for kidney stone disease in humans. OOR catalyzes the anaerobic oxidation of oxalate, harvesting the low-potential electrons for use in anaerobic reduction and fixation of CO2. We compare the OOR structure to that of the only other structurally characterized OFOR family member, pyruvate:ferredoxin oxidoreductase. This side-by-side structural analysis highlights the key similarities and differences that are relevant for the chemistry of this entire class of TPP-utilizing enzymes.


    Organizational Affiliation

    †Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxalate oxidoreductase subunit alpha
A, D
395Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
EC: 1.2.7.10
Find proteins for Q2RI41 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q2RI41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Oxalate oxidoreductase subunit delta
B, E
315Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
EC: 1.2.7.10
Find proteins for Q2RI40 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q2RI40
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Oxalate oxidoreductase subunit beta
C, F
314Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
EC: 1.2.7.10
Find proteins for Q2RI42 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q2RI42
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
C, F
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
B, C, E, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.274 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.351α = 90.00
b = 152.203β = 90.00
c = 171.824γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM069857
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM39451
National Science Foundation (United States)United States1122374
Howard Hughes Medical InstituteUnited States--
Martin 592 Family Society of Fellows for SustainabilityUnited States--

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2016-03-16
    Type: Data collection
  • Version 1.3: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Refinement description