6CIQ

Pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica with coenzyme A bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.302 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Binding site for coenzyme A revealed in the structure of pyruvate:ferredoxin oxidoreductase fromMoorella thermoacetica.

Chen, P.Y.Aman, H.Can, M.Ragsdale, S.W.Drennan, C.L.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 3846-3851

  • DOI: 10.1073/pnas.1722329115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyruvate:ferredoxin oxidoreductase (PFOR) is a microbial enzyme that uses thiamine pyrophosphate (TPP), three [4Fe-4S] clusters, and coenzyme A (CoA) in the reversible oxidation of pyruvate to generate acetyl-CoA and carbon dioxide. The two electrons ...

    Pyruvate:ferredoxin oxidoreductase (PFOR) is a microbial enzyme that uses thiamine pyrophosphate (TPP), three [4Fe-4S] clusters, and coenzyme A (CoA) in the reversible oxidation of pyruvate to generate acetyl-CoA and carbon dioxide. The two electrons that are generated as a result of pyruvate decarboxylation are used in the reduction of low potential ferredoxins, which provide reducing equivalents for central metabolism, including the Wood-Ljungdahl pathway. PFOR is a member of the 2-oxoacid:ferredoxin oxidoreductase (OFOR) superfamily, which plays major roles in both microbial redox reactions and carbon dioxide fixation. Here, we present a set of crystallographic snapshots of the best-studied member of this superfamily, the PFOR from Moorella thermoacetica ( Mt PFOR). These snapshots include the native structure, those of lactyl-TPP and acetyl-TPP reaction intermediates, and the first of an OFOR with CoA bound. These structural data reveal the binding site of CoA as domain III, the function of which in OFORs was previously unknown, and establish sequence motifs for CoA binding in the OFOR superfamily. Mt PFOR structures further show that domain III undergoes a conformational change upon CoA binding that seals off the active site and positions the thiolate of CoA directly adjacent to the TPP cofactor. These structural findings provide a molecular basis for the experimental observation that CoA binding accelerates catalysis by 10 5 -fold.


    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139; cdrennan@mit.edu.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRUVATE-FERREDOXIN OXIDOREDUCTASE
A, B, C
1171Moorella thermoacetica (strain ATCC 39073 / JCM 9320)Mutation(s): 0 
EC: 1.2.7.1
Find proteins for Q2RMD6 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Go to UniProtKB:  Q2RMD6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download SDF File 
Download CCD File 
A, B, C
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, B, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B, C
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.302 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 337.710α = 90.00
b = 106.993β = 109.85
c = 120.465γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references
  • Version 1.3: 2018-10-03
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.5: 2020-01-01
    Type: Author supporting evidence