5EXE

Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-TPP adduct


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.

Gibson, M.I.Chen, P.Y.Johnson, A.C.Pierce, E.Can, M.Ragsdale, S.W.Drennan, C.L.

(2016) Proc Natl Acad Sci U S A 113: 320-325

  • DOI: 10.1073/pnas.1518537113
  • Primary Citation of Related Structures:  
    5EXE, 5EXD

  • PubMed Abstract: 
  • Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2 and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood-Ljungdahl path ...

    Thiamine pyrophosphate (TPP)-dependent oxalate oxidoreductase (OOR) metabolizes oxalate, generating two molecules of CO2 and two low-potential electrons, thus providing both the carbon and reducing equivalents for operation of the Wood-Ljungdahl pathway of acetogenesis. Here we present structures of OOR in which two different reaction intermediate bound states have been trapped: the covalent adducts between TPP and oxalate and between TPP and CO2. These structures, along with the previously determined structure of substrate-free OOR, allow us to visualize how active site rearrangements can drive catalysis. Our results suggest that OOR operates via a bait-and-switch mechanism, attracting substrate into the active site through the presence of positively charged and polar residues, and then altering the electrostatic environment through loop and side chain movements to drive catalysis. This simple but elegant mechanism explains how oxalate, a molecule that humans and most animals cannot break down, can be used for growth by acetogenic bacteria.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 cdrennan@mit.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit alphaAD395Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1592
EC: 1.2.7.10
Find proteins for Q2RI41 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI41 
Go to UniProtKB:  Q2RI41
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit deltaBE315Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1593
EC: 1.2.7.10
Find proteins for Q2RI40 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI40 
Go to UniProtKB:  Q2RI40
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit betaCF314Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1591
EC: 1.2.7.10
Find proteins for Q2RI42 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI42 
Go to UniProtKB:  Q2RI42
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5SR
Query on 5SR

Download CCD File 
C, F
[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-carboxy-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-oxidanyl-phosphoryl] hydrogen phosphate
C13 H18 N4 O9 P2 S
SXXTZHDPRYKKAS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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B, C, E, F
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MG
Query on MG

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C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.653α = 90
b = 144.131β = 90
c = 161.715γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Data collection
  • Version 1.2: 2016-01-27
    Changes: Database references