4WYS | pdb_00004wys

Crystal structure of thiolase from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb4WYS/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-18 Released: 2015-10-07 
• Deposition Author(s): Kim, S., Ha, S.C., Ahn, J.W., Kim, E.J., Lim, J.H., Kim, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum

Kim, S., Jang, Y.S., Ha, S.C., Ahn, J.W., Kim, E.J., Hong Lim, J., Cho, C., Shin Ryu, Y., Kuk Lee, S., Lee, S.Y., Kim, K.J.

(2015) Nat Commun 6: 8410-8410

• PubMed: 26391388 
• DOI: https://doi.org/10.1038/ncomms9410
• Primary Citation Related Structures: 
  4WYR, 4WYS, 4XL2, 4XL3, 4XL4


• PubMed Abstract: 
  

  Thiolase is the first enzyme catalysing the condensation of two acetyl-coenzyme A (CoA) molecules to form acetoacetyl-CoA in a dedicated pathway towards the biosynthesis of n-butanol, an important solvent and biofuel. Here we elucidate the crystal structure of Clostridium acetobutylicum thiolase (CaTHL) in its reduced/oxidized states. CaTHL, unlike those from other aerobic bacteria such as Escherichia coli and Zoogloea ramegera, is regulated by the redox-switch modulation through reversible disulfide bond formation between two catalytic cysteine residues, Cys88 and Cys378. When CaTHL is overexpressed in wild-type C. acetobutylicum, butanol production is reduced due to the disturbance of acidogenic to solventogenic shift. The CaTHL(V77Q/N153Y/A286K) mutant, which is not able to form disulfide bonds, exhibits higher activity than wild-type CaTHL, and enhances butanol production upon overexpression. On the basis of these results, we suggest that CaTHL functions as a key enzyme in the regulation of the main metabolism of C. acetobutylicum through a redox-switch regulatory mechanism.

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Organizational Affiliation: 
• School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea.
School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 689-798, Korea.
Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and BioProcess Engineering Research Center, KAIST, Daejeon 305-701, Korea.
Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Korea.
Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, and Bioinformatics Research Center, KAIST, Daejeon 305-701, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 166.88 kDa 
• Atom Count: 12,024 
• Modeled Residue Count: 1,584 
• Deposited Residue Count: 1,620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B, C, D	405	Escherichia coli K-12	Mutation(s): 0  Gene Names: atoB, b2224, JW2218 EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12)) Explore P76461  Go to UniProtKB:  P76461

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.007	α = 90
b = 85.151	β = 90
c = 269.113	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Kim, S., Ha, S.C., Ahn, J.W., Kim, E.J., Lim, J.H., Kim, K.J.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description