Crystal structure of beta-ketothiolase BktB B from Ralstonia eutropha H16

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.265 

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Crystal structure and biochemical characterization of beta-keto thiolase B from polyhydroxyalkanoate-producing bacterium Ralstonia eutropha H16

Kim, E.J.Son, H.F.Kim, S.Ahn, J.W.Kim, K.J.

(2014) Biochem Biophys Res Commun 444: 365-369

  • DOI: https://doi.org/10.1016/j.bbrc.2014.01.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    ReBktB is a β-keto thiolase from Ralstonia eutropha H16 that catalyzes condensation reactions between acetyl-CoA with acyl-CoA molecules that contains different numbers of carbon atoms, such as acetyl-CoA, propionyl-CoA, and butyryl-CoA, to produce valuable bioproducts, such as polyhydroxybutyrate, polyhydroxybutyrate-hydroxyvalerate, and hexanoate. We solved a crystal structure of ReBktB at 2.3Å, and the overall structure has a similar fold to that of type II biosynthetic thiolases, such as PhbA from Zoogloea ramigera (ZrPhbA). The superposition of this structure with that of ZrPhbA complexed with CoA revealed the residues that comprise the catalytic and substrate binding sites of ReBktB. The catalytic site of ReBktB contains three conserved residues, Cys90, His350, and Cys380, which may function as a covalent nucleophile, a general base, and second nucleophile, respectively. For substrate binding, ReBktB stabilized the ADP moiety of CoA in a distinct way compared to ZrPhbA with His219, Arg221, and Asp228 residues, whereas the stabilization of β-mercaptoethyamine and pantothenic acid moieties of CoA was quite similar between these two enzymes. Kinetic study of ReBktB revealed that K(m), V(max), and K(cat) values of 11.58 μM, 1.5 μmol/min, and 102.18 s(-1), respectively, and the catalytic and substrate binding sites of ReBktB were further confirmed by site-directed mutagenesis experiments.

  • Organizational Affiliation

    Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-ketothiolase BktB
A, B
399Cupriavidus necator H16Mutation(s): 0 
Gene Names: bktBH16_A1445
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q0KBP1 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337))
Explore Q0KBP1 
Go to UniProtKB:  Q0KBP1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0KBP1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.265 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.954α = 90
b = 107.236β = 90
c = 144.137γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 2.0: 2017-11-22
    Changes: Atomic model, Derived calculations, Refinement description
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description