5EXD image
Deposition Date 2015-11-23
Release Date 2015-12-30
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5EXD
Keywords:
Title:
Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate
Biological Source:
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 43
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxalate oxidoreductase subunit alpha
Gene (Uniprot):Moth_1592
Chain IDs:A, D, G, J
Chain Length:395
Number of Molecules:4
Biological Source:Moorella thermoacetica (strain ATCC 39073)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxalate oxidoreductase subunit delta
Gene (Uniprot):Moth_1593
Chain IDs:B, E, H, K
Chain Length:315
Number of Molecules:4
Biological Source:Moorella thermoacetica (strain ATCC 39073)
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Oxalate oxidoreductase subunit beta
Gene (Uniprot):Moth_1591
Chain IDs:C, F, I, L
Chain Length:314
Number of Molecules:4
Biological Source:Moorella thermoacetica (strain ATCC 39073)
Primary Citation
One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography.
Proc.Natl.Acad.Sci.USA 113 320 325 (2016)
PMID: 26712008 DOI: 10.1073/pnas.1518537113

Abstact

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.

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