5C4I

Structure of an Oxalate Oxidoreductase


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 

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Ligand Structure Quality Assessment 


This is version 1.4 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
  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit alphaA, D395Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1592
EC: 1.2.7.10
UniProt
Find proteins for Q2RI41 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI41 
Go to UniProtKB:  Q2RI41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RI41
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit deltaB, E315Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1593
EC: 1.2.7.10
UniProt
Find proteins for Q2RI40 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI40 
Go to UniProtKB:  Q2RI40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RI40
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Oxalate oxidoreductase subunit betaC, F314Moorella thermoacetica ATCC 39073Mutation(s): 0 
Gene Names: Moth_1591
EC: 1.2.7.10
UniProt
Find proteins for Q2RI42 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RI42 
Go to UniProtKB:  Q2RI42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RI42
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
K [auth C],
P [auth F]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
J [auth C],
M [auth E],
N [auth E],
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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth C],
Q [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth B],
R [auth F]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 84.351α = 90
b = 152.203β = 90
c = 171.824γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM39451
National Science Foundation (NSF, United States)United States1122374
Howard Hughes Medical Institute (HHMI)United States--
Martin 592 Family Society of Fellows for SustainabilityUnited States--

Revision History  (Full details and data files)

  • 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