Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (orthorombic form)

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold for an Uncommon Claisen-Type Condensation.

Bellinzoni, M.Bastard, K.Perret, A.Zaparucha, A.Perchat, N.Vergne, C.Wagner, T.De Melo-Minardi, R.C.Artiguenave, F.Cohen, G.N.Weissenbach, J.Salanoubat, M.Alzari, P.M.

(2011) J Biol Chem 286: 27399

  • DOI: https://doi.org/10.1074/jbc.M111.253260
  • Primary Citation of Related Structures:  
    2Y7D, 2Y7E, 2Y7F, 2Y7G

  • PubMed Abstract: 

    The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn(2+) cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the "domain of unknown function" DUF849.

  • Organizational Affiliation

    Unité de Microbiologie Structurale, Institut Pasteur, and CNRS-URA2185, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
282Candidatus Cloacimonas acidaminovoransMutation(s): 0 
Find proteins for B0VHH0 (Cloacimonas acidaminovorans (strain Evry))
Explore B0VHH0 
Go to UniProtKB:  B0VHH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0VHH0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.87α = 90
b = 100.82β = 90
c = 147.43γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references, Version format compliance