8JG2 | pdb_00008jg2

Crystal structure of a biosynthetic thiolase from Megasphaera hexanoica soaked with hexanoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.236 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Molecular Chain Elongation Mechanism for n-Caproate Biosynthesis by Megasphaera Hexanoica.

Jeon, B.S.Kim, E.J.Seo, H.Kim, H.Shin, S.Schlaiss, C.Angenent, L.T.Kim, K.J.Sang, B.I.

(2025) Adv Sci (Weinh) : e06069-e06069

  • DOI: https://doi.org/10.1002/advs.202506069
  • Primary Citation Related Structures: 
    8JG2, 8JG3

  • PubMed Abstract: 

    The microbial production of medium-chain carboxylates has attracted considerable interest owing to their potential applications in biofuels and specialty chemicals; however, the underlying biosynthetic mechanisms remain incompletely understood. The present study evaluates the medium-chain carboxylate-producing microbe Megaspahera hexanoica using genomic analysis, transcriptome analysis, and metabolic engineering. Additionally, the n-caproate synthesis pathway of M. hexanoica is characterized with fructose as an electron donor, and the substrate specificity of the respective proteins is evaluated by constructing an n-caproate biosynthetic pathway in Escherichia coli. Among all r-BOX or RBO genes, thl_1583, which encodes β-ketothiolase (MhTHL), is identified as the most critical enzyme for the carbon chain elongation mechanism in M. hexanoica. Therefore, MhTHL is compared with other well-studied β-ketothiolases (CkTHL from Clostridium kluyveri, ReBktB from Ralstonia eutropha (Cupriavidus necator), EcAtoB from E. coli, and CaTHL from C. acetobutylicum). MhTHL is found to exhibit the highest n-caproate production, as evidenced by the protein crystal structure of MhTHL. Structural comparisons with other thiolases show that MhTHL has a larger substrate-binding pocket than ReBktB. Thiolase mutants generated by site-directed mutagenesis reveal that two residues (Leu87 and Val351) are essential for determining the size of the substrate-binding pocket.


  • Organizational Affiliation
    • Korea Institute of Ceramic Engineering and Technology, Osong, 28160, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 93.84 kDa 
  • Atom Count: 6,536 
  • Modeled Residue Count: 786 
  • Deposited Residue Count: 868 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetyl-CoA C-acetyltransferase
A, B
434Megasphaera hexanoicaMutation(s): 1 
Gene Names: HF872_02440
EC: 2.3.1.9
UniProt
Find proteins for A0A848BQU5 (Megasphaera hexanoica)
Explore A0A848BQU5 
Go to UniProtKB:  A0A848BQU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A848BQU5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.236 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.505α = 90
b = 111.443β = 90
c = 140.996γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references, Structure summary