4W61 | pdb_00004w61

Crystal structure of beta-ketoacyl thiolase B (BktB) from Ralstonia eutropha


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.208 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Coenzyme A-free activity, crystal structure, and rational engineering of a promiscuous beta-ketoacyl thiolase fromRalstonia eutropha.

Fage, C.D.Meinke, J.L.Keatinge-Clay, A.T.

(2015) J Mol Catal B Enzym 121: 113-121

  • DOI: https://doi.org/10.1016/j.molcatb.2015.08.007
  • Primary Citation Related Structures: 
    4W61

  • PubMed Abstract: 

    Thiolases catalyze the formation of carbon-carbon bonds in diverse biosynthetic pathways. The promiscuous β-ketoacyl thiolase B of Ralstonia eutropha ( Re BktB) has been utilized in the in vivo conversion of Coenzyme A (CoA)-linked precursors such as acetyl-CoA and glycolyl-CoA into β-hydroxy acids, including the pharmaceutically-important 3,4-dihydroxybutyric acid. Such thiolases could serve as powerful carbon-carbon bond-forming biocatalysts in vitro if handles less costly than CoA were employable. Here, thiolase activity is demonstrated toward substrates linked to the readily-available CoA mimic, N -acetylcysteamine (NAC). Re BktB was observed to catalyze the retro-Claisen condensation of several β-ketoacyl- S -NAC substrates, with a preference for 3-oxopentanoyl- S -NAC over 3-oxobutanoyl-, 3-oxohexanoyl-, and 3-oxoheptanoyl- S -NAC. A 2.0 Å-resolution crystal structure, in which the asymmetric unit consists of four Re BktB tetramers, provides insight into acyl group specificity and how it may be engineered. By replacing an active site methionine with an alanine, a mutant possessing significant activity towards α-methyl substituted, NAC-linked substrates was engineered. The ability of Re BktB and its engineered mutants to utilize NAC-linked substrates will facilitate the in vitro biocatalytic synthesis of diketide chiral building blocks from feedstock molecules such as acetate and propionate.


  • Organizational Affiliation
    • Department of Molecular Biosciences, The University of Texas, Austin, TX 78712, USA.

Macromolecule Content 

  • Total Structure Weight: 689.99 kDa 
  • Atom Count: 46,062 
  • Modeled Residue Count: 6,237 
  • Deposited Residue Count: 6,624 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-ketothiolase BktB
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
414Cupriavidus necator H16Mutation(s): 0 
Gene Names: bktBH16_A1445
EC: 2.3.1.16 (PDB Primary Data), 2.3.1.9 (PDB Primary Data)
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.208 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.05α = 89.97
b = 105.987β = 89.98
c = 201.142γ = 89.93
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106112

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence, Source and taxonomy
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description