Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 227.01 kDa 
• Atom Count: 17286 
• Modelled Residue Count: 2031 
• Deposited Residue Count: 2048 
• Unique protein chains: 3

5C4I

Structure of an Oxalate Oxidoreductase

• DOI: 10.2210/pdb5C4I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Moorella thermoacetica ATCC 39073
• Mutation(s): No 


• Deposited: 2015-06-18 Released: 2015-07-01 
• Deposition Author(s): Gibson, M.I., Brignole, E.J., Pierce, E., Can, M., Ragsdale, S.W., Drennan, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI), Martin 592 Family Society of Fellows for Sustainability

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

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

• PubMed: 26061898 
• DOI: 10.1021/acs.biochem.5b00521
• Primary Citation of Related Structures:  
  5C4I


• 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 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 Å) 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.

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Organizational Affiliation: 

∥Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate oxidoreductase subunit alpha	A, D	395	Moorella thermoacetica ATCC 39073	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate oxidoreductase subunit delta	B, E	315	Moorella thermoacetica ATCC 39073	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxalate oxidoreductase subunit beta	C, F	314	Moorella thermoacetica ATCC 39073	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TPP	K [auth C], P [auth F]	THIAMINE DIPHOSPHATE C12 H19 N4 O7 P2 S AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4	G [auth B], H [auth B], J [auth C], M [auth E], N [auth E], O [auth F]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
MG	L [auth C], Q [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	I [auth B], R [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.216 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.351	α = 90
b = 152.203	β = 90
c = 171.824	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-06-18 
• Released Date: 2015-07-01 
Deposition Author(s): Gibson, M.I., Brignole, E.J., Pierce, E., Can, M., Ragsdale, S.W., Drennan, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM39451
National Science Foundation (NSF, United States)	United States	1122374
Howard Hughes Medical Institute (HHMI)	United States	--
Martin 592 Family Society of Fellows for Sustainability	United States	--

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Database references
• Version 1.2: 2016-03-16
  Changes: Data collection
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.4: 2019-11-20
  Changes: Author supporting evidence