1P5R

Formyl-CoA Transferase in complex with Coenzyme A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Formyl-CoA Transferase encloses the CoA binding site at the interface of an interlocked dimer

Ricagno, S.Jonsson, S.Richards, N.Lindqvist, Y.

(2003) EMBO J 22: 3210-3219

  • DOI: https://doi.org/10.1093/emboj/cdg333
  • Primary Citation of Related Structures:  
    1P5H, 1P5R

  • PubMed Abstract: 

    Formyl-CoA transferase catalyses transfer of CoA from formate to oxalate in the first step of oxalate degradation by Oxalobacter formigenes, a bacterium present in the intestinal flora which is implicated in oxalate catabolism in mammals. Formyl-CoA transferase is a member of a family of CoA-transferases for which no structural information is available. We now report the three-dimensional structure of O.formigenes formyl-CoA transferase, which reveals a novel fold and a very striking assembly of the homodimer. The subunit is composed of a large and a small domain where residues from both the N- and C-termini of the subunit are part of the large domain. The linkers between the domains give the subunit a circular shape with a hole in the middle. The enzyme monomers are tightly interacting and are interlocked. This fold requires drastic rearrangement of approximately 75 residues at the C-terminus for formation of the dimer. The structure of a complex of formyl-CoA transferase with CoA is also reported and sets the scene for a mechanistic understanding of enzymes of this family of CoA-transferases.


  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formyl-coenzyme A transferase
A, B
428Oxalobacter formigenesMutation(s): 0 
Gene Names: FRC
EC: 2.8.3 (PDB Primary Data), 2.8.3.16 (UniProt)
UniProt
Find proteins for O06644 (Oxalobacter formigenes)
Explore O06644 
Go to UniProtKB:  O06644
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06644
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.4α = 90
b = 151.4β = 90
c = 99.5γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description