Crystal structure of 4-hydroxybutyrate CoA-Transferase from Clostridium aminobutyricum

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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Crystal structure of 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum

Macieira, S.Zhang, J.Velarde, M.Buckel, W.Messerschmidt, A.

(2009) Biol Chem 390: 1251-1263

  • DOI: https://doi.org/10.1515/BC.2009.147
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    4-Hydroxybutyrate CoA-transferases (4-HB-CoAT) takes part in the fermentation of 4-aminobutyrate to ammonia, acetate, and butyrate in anaerobic bacteria such as Clostridium aminobutyricum and Porphyromonas gingivalis or facultative anaerobic bacteria such as Shewanella oneidensis. Site-directed mutagenesis of the highly active enzyme has identified the catalytic glutamate residue as E238. Crystal structure of this enzyme has been determined at a resolution of 1.85 A. The 438-amino acid residue polypeptide chain folds into two topologically similar domains with an open alpha/beta-fold, which is also found in other CoAT family I and family II members. The data indicate that the members of CoAT families I and II are closely related; the latter only lacking the catalytic glutamate residue. A putative co-substrate binding site for the 4-HB-CoAT was identified, in which a 4-hydroxybutyrate molecule has been modeled. This site is also responsible for binding the acetyl group of acetyl-CoA or the succinyl group of succinyl-CoA in succinyl-CoA:3-oxoacid CoA-transferase from mammalian mitochondria. Mutations of relevant active site amino acid residues have been produced and their activities tested to corroborate the proposed structural model for substrate binding. 4-HB-CoAT from C. aminobutyricum represents the only functionally characterized 4-HB-CoAT present in the structural database.

  • Organizational Affiliation

    Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-Hydroxybutyrate CoA-transferase
A, B
448Clostridium aminobutyricumMutation(s): 0 
Gene Names: abfT
EC: 2.8.3
Find proteins for Q9RM86 (Clostridium aminobutyricum)
Explore Q9RM86 
Go to UniProtKB:  Q9RM86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RM86
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.589α = 90
b = 116.589β = 90
c = 174.328γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description