9BT4

Pyruvate:Ferredoxin Oxidoreductase from Methanosarcina acetivorans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.174 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structural organization of pyruvate: ferredoxin oxidoreductase from the methanogenic archaeon Methanosarcina acetivorans.

Cossu, M.Catlin, D.Elliott, S.J.Metcalf, W.W.Nair, S.K.

(2024) Structure 32: 1963

  • DOI: https://doi.org/10.1016/j.str.2024.08.011
  • Primary Citation of Related Structures:  
    9BT4

  • PubMed Abstract: 

    Enzymes of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily catalyze the reversible oxidation of 2-oxoacids to acyl-coenzyme A esters and carbon dioxide (CO 2 )using ferredoxin or flavodoxin as the redox partner. Although members of the family share primary sequence identity, a variety of domain and subunit arrangements are known. Here, we characterize the structure of a four-subunit family member: the pyruvate:ferredoxin oxidoreductase (PFOR) from the methane producing archaeon Methanosarcina acetivorans (MaPFOR). The 1.92 Å resolution crystal structure of MaPFOR shows a protein fold like those of single- or two-subunit PFORs that function in 2-oxoacid oxidation, including the location of the requisite thiamine pyrophosphate (TPP), and three [4Fe-4S] clusters. Of note, MaPFOR typically functions in the CO 2 reductive direction, and structural comparisons to the pyruvate oxidizing PFORs show subtle differences in several regions of catalytical relevance. These studies provide a framework that may shed light on the biochemical mechanisms used to facilitate reductive pyruvate synthesis.


  • Organizational Affiliation

    Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate:Ferredoxin Oxidoreductase, subunit alphaA [auth B],
B [auth A]
403Methanosarcina acetivorans C2AMutation(s): 0 
EC: 1.2.7.1
UniProt
Find proteins for Q8TUN4 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TUN4 
Go to UniProtKB:  Q8TUN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TUN4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate:Ferredoxin Oxidoreductase, subunit beta
C, D
296Methanosarcina acetivorans C2AMutation(s): 0 
UniProt
Find proteins for Q8TUN5 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TUN5 
Go to UniProtKB:  Q8TUN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TUN5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate:Ferredoxin Oxidoreductase, subunit deltaE [auth G],
F [auth H]
85Methanosarcina acetivorans C2AMutation(s): 0 
UniProt
Find proteins for Q8TUN3 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TUN3 
Go to UniProtKB:  Q8TUN3
Entity Groups  
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UniProt GroupQ8TUN3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate:Ferredoxin Oxidoreductase, subunit gammaG [auth E],
H [auth F]
182Methanosarcina acetivorans C2AMutation(s): 0 
EC: 1.2.7.1
UniProt
Find proteins for Q8TUN2 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A))
Explore Q8TUN2 
Go to UniProtKB:  Q8TUN2
Entity Groups  
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UniProt GroupQ8TUN2
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP (Subject of Investigation/LOI)
Query on TPP

Download Ideal Coordinates CCD File 
J [auth C],
M [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
I [auth C]
L [auth D]
O [auth G]
P [auth G]
Q [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
K [auth C],
N [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.200 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.121α = 90
b = 79.121β = 90
c = 496.524γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted TPPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-FG02-02ER15296

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-09
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references