4XL4 | pdb_00004xl4

Crystal structure of thiolase from Clostridium acetobutylicum in complex with CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.183 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

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

  • 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.


  • Organizational Affiliation
    • School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea.

Macromolecule Content 

  • Total Structure Weight: 86.87 kDa 
  • Atom Count: 6,611 
  • Modeled Residue Count: 784 
  • Deposited Residue Count: 800 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferase
A, B
400Clostridium acetobutylicum EA 2018Mutation(s): 1 
Gene Names: CEA_G2880
EC: 2.3.1.9
UniProt
Find proteins for A0A0R4I970 (Clostridium acetobutylicum (strain EA 2018))
Explore A0A0R4I970 
Go to UniProtKB:  A0A0R4I970
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0R4I970
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA

Query on COA



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.183 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.154 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.307α = 90
b = 54.171β = 90
c = 73.112γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description