1P5R | pdb_00001p5r

Formyl-CoA Transferase in complex with Coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb1P5R/pdb

• Classification: TRANSFERASE
• Organism(s): Oxalobacter formigenes
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-04-28 Released: 2003-07-29 
• Deposition Author(s): Ricagno, S., Jonsson, S., Richards, N., Lindqvist, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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

• PubMed: 12839984 
• DOI: https://doi.org/10.1093/emboj/cdg333
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-17177 Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 96.3 kDa 
• Atom Count: 6,982 
• Modeled Residue Count: 854 
• Deposited Residue Count: 856 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Formyl-coenzyme A transferase	A, B	428	Oxalobacter formigenes	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	C [auth A], D [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.4	α = 90
b = 151.4	β = 90
c = 99.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-29 
Deposition Author(s): Ricagno, S., Jonsson, S., Richards, N., Lindqvist, Y.

Revision History  

• 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