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PDBsum entry 1t4c

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protein ligands Protein-protein interface(s) links
Transferase PDB id
1t4c
Jmol
Contents
Protein chains
427 a.a. *
Ligands
COA ×2
Waters ×130
* Residue conservation analysis
PDB id:
1t4c
Name: Transferase
Title: Formyl-coa transferase in complex with oxalyl-coa
Structure: Formyl-coenzyme a transferase. Chain: a. Synonym: formyl-coa transferase. Engineered: yes. Formyl-coenzyme a transferase. Chain: b. Synonym: formyl-coa transferase. Engineered: yes
Source: Oxalobacter formigenes. Organism_taxid: 847. Gene: frc. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
Resolution:
2.61Å     R-factor:   0.204     R-free:   0.273
Authors: S.Ricagno,S.Jonsson,N.G.Richards,Y.Lindqvist
Key ref:
S.Jonsson et al. (2004). Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes. J Biol Chem, 279, 36003-36012. PubMed id: 15213226 DOI: 10.1074/jbc.M404873200
Date:
29-Apr-04     Release date:   03-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O06644  (FCTA_OXAFO) -  Formyl-coenzyme A transferase
Seq:
Struc:
428 a.a.
427 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.8.3.16  - Formyl-CoA transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formyl-CoA + oxalate = formate + oxalyl-CoA
Formyl-CoA
Bound ligand (Het Group name = COA)
matches with 96.00% similarity
+ oxalate
= formate
+ oxalyl-CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M404873200 J Biol Chem 279:36003-36012 (2004)
PubMed id: 15213226  
 
 
Kinetic and mechanistic characterization of the formyl-CoA transferase from Oxalobacter formigenes.
S.Jonsson, S.Ricagno, Y.Lindqvist, N.G.Richards.
 
  ABSTRACT  
 
Oxalobacter formigenes is an obligate anaerobe that colonizes the human gastrointestinal tract and employs oxalate breakdown to generate ATP in a novel process involving the interplay of two coupled enzymes and a membrane-bound oxalate:formate antiporter. Formyl-CoA transferase is a critical enzyme in oxalate-dependent ATP synthesis and is the first Class III CoA-transferase for which a high resolution, three-dimensional structure has been determined (Ricagno, S., Jonsson, S., Richards, N., and Lindqvist, Y. (2003) EMBO J. 22, 3210-3219). We now report the first detailed kinetic characterizations of recombinant, wild type formyl-CoA transferase and a number of site-specific mutants, which suggest that catalysis proceeds via a series of anhydride intermediates. Further evidence for this mechanistic proposal is provided by the x-ray crystallographic observation of an acylenzyme intermediate that is formed when formyl-CoA transferase is incubated with oxalyl-CoA. The catalytic mechanism of formyl-CoA transferase is therefore established and is almost certainly employed by all other members of the Class III CoA-transferase family.
 
  Selected figure(s)  
 
Figure 5.
FIG. 5. Proposed catalytic mechanism of O. formigenes FRC. The box highlights the anhydride intermediate that is crystallographically observed (see below) and shown in Fig. 7.
Figure 7.
FIG. 7. The active site in FRC-oxalyl-CoA complex, monomer B. A, divergent eyes stereo view showing the interactions of the oxalylaspartyl anhydride with residues in the FRC dimer. The letter designation (A or B) in the numbering scheme indicates the FRC monomer in which the residue is located. This image was generated using VMD (58) and POV-Ray (Persistence of Vision Development Team). B, initial difference Fourier electron density map at 2.5 of the oxalyl-aspartyl anhydride. This image was generated using MOLSCRIPT (59) and Raster-3D (60).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 36003-36012) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20553497 T.Werther, A.Zimmer, G.Wille, R.Golbik, M.S.Weiss, and S.König (2010).
New insights into structure-function relationships of oxalyl CoA decarboxylase from Escherichia coli.
  FEBS J, 277, 2628-2640.
PDB codes: 2q27 2q28 2q29
19955419 J.Zarzycki, V.Brecht, M.Müller, and G.Fuchs (2009).
Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.
  Proc Natl Acad Sci U S A, 106, 21317-21322.  
19078968 K.Sakhaee (2009).
Recent advances in the pathophysiology of nephrolithiasis.
  Kidney Int, 75, 585-595.  
19095203 K.Sakhaee (2009).
Pharmacology of stone disease.
  Adv Chronic Kidney Dis, 16, 30-38.  
18245280 C.G.Toyota, C.L.Berthold, A.Gruez, S.Jónsson, Y.Lindqvist, C.Cambillau, and N.G.Richards (2008).
Differential substrate specificity and kinetic behavior of Escherichia coli YfdW and Oxalobacter formigenes formyl coenzyme A transferase.
  J Bacteriol, 190, 2556-2564.
PDB codes: 2vjp 2vjq
18279392 M.D.Lloyd, D.J.Darley, A.S.Wierzbicki, and M.D.Threadgill (2008).
Alpha-methylacyl-CoA racemase--an 'obscure' metabolic enzyme takes centre stage.
  FEBS J, 275, 1089-1102.  
17827318 B.Sánchez, M.C.Champomier-Vergès, B.Stuer-Lauridsen, P.Ruas-Madiedo, P.Anglade, F.Baraige, C.G.de los Reyes-Gavilán, E.Johansen, M.Zagorec, and A.Margolles (2007).
Adaptation and response of Bifidobacterium animalis subsp. lactis to bile: a proteomic and physiological approach.
  Appl Environ Microbiol, 73, 6757-6767.  
17953571 S.Turroni, B.Vitali, C.Bendazzoli, M.Candela, R.Gotti, F.Federici, F.Pirovano, and P.Brigidi (2007).
Oxalate consumption by lactobacilli: evaluation of oxalyl-CoA decarboxylase and formyl-CoA transferase activity in Lactobacillus acidophilus.
  J Appl Microbiol, 103, 1600-1609.  
16957230 J.Kim, D.Darley, T.Selmer, and W.Buckel (2006).
Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile.
  Appl Environ Microbiol, 72, 6062-6069.  
16755588 K.S.Lee, S.M.Park, K.H.Rhee, W.G.Bang, K.Y.Hwang, and Y.M.Chi (2006).
Crystal structure of fatty acid-CoA racemase from Mycobacterium tuberculosis H37Rv.
  Proteins, 64, 817-822.
PDB code: 2g04
16547052 S.Friedmann, A.Steindorf, B.E.Alber, and G.Fuchs (2006).
Properties of succinyl-coenzyme A:L-malate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 188, 2646-2655.  
16952935 S.Friedmann, B.E.Alber, and G.Fuchs (2006).
Properties of succinyl-coenzyme A:D-citramalate coenzyme A transferase and its role in the autotrophic 3-hydroxypropionate cycle of Chloroflexus aurantiacus.
  J Bacteriol, 188, 6460-6468.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.