2VJM

Formyl-CoA transferase with aspartyl-formyl anhydide intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, a Class III Coa-Transferase.

Berthold, C.L.Toyota, C.G.Richards, N.G.J.Lindqvist, Y.

(2008) J.Biol.Chem. 283: 6519

  • DOI: 10.1074/jbc.M709353200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transfe ...

    Formyl-coenzyme A transferase from Oxalobacter formigenes belongs to the Class III coenzyme A transferase family and catalyzes the reversible transfer of a CoA carrier between formyl-CoA and oxalate, forming oxalyl-CoA and formate. Formyl-CoA transferase has a unique three-dimensional fold composed of two interlaced subunits locked together like rings of a chain. We here present an intermediate in the reaction, formyl-CoA transferase containing the covalent beta-aspartyl-CoA thioester, adopting different conformations in the two active sites of the dimer, which was identified through crystallographic freeze-trapping experiments with formyl-CoA and oxalyl-CoA in the absence of acceptor carboxylic acid. The formation of the enzyme-CoA thioester was also confirmed by mass spectrometric data. Further structural data include a trapped aspartyl-formyl anhydride protected by a glycine loop closing down over the active site. In a crystal structure of the beta-aspartyl-CoA thioester of an inactive mutant variant, oxalate was found bound to the open conformation of the glycine loop. Together with hydroxylamine trapping experiments and kinetic as well as mutagenesis data, the structures of these formyl-CoA transferase complexes provide new information on the Class III CoA-transferase family and prompt redefinition of the catalytic steps and the modified reaction mechanism of formyl-CoA transferase proposed here.


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Molecular Structural Biology, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FORMYL-COENZYME A TRANSFERASE
A
428Oxalobacter formigenesMutation(s): 0 
Gene Names: frc
EC: 2.8.3.16
Find proteins for O06644 (Oxalobacter formigenes)
Go to UniProtKB:  O06644
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FORMYL-COENZYME A TRANSFERASE
B
428Oxalobacter formigenesMutation(s): 0 
Gene Names: frc
EC: 2.8.3.16
Find proteins for O06644 (Oxalobacter formigenes)
Go to UniProtKB:  O06644
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
A0A
Query on A0A
B
non-polymerC5 H7 N O5

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 151.668α = 90.00
b = 151.668β = 90.00
c = 98.947γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Advisory, Data collection