8K1C | pdb_00008k1c

Structural insight into the role of acetyl-CoA acetyltransferase from Fusobacterium nucleatum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.243 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insight into the role of thiolase from Fusobacterium nucleatum.

He, S.Bai, X.Xu, Y.

(2023) Biochem Biophys Res Commun 688: 149151-149151

  • DOI: https://doi.org/10.1016/j.bbrc.2023.149151
  • Primary Citation of Related Structures:  
    8K1C

  • PubMed Abstract: 

    Fusobacterium nucleatum (F. nucleatum) is an anaerobic gram-negative bacterium that was previously thought to be related to the progression of colorectal cancer. In F. nucleatum, thiolase participates in fatty acid metabolism, and it can catalyse the transfer of an acetyl group from acetyl-CoA to another molecule, typically a fatty acid or another molecule in the synthesis of lipids. To gain deeper insight into the molecular mechanism governing the function of thiolase in F. nucleatum (Fn0495), we herein report the structure of Fn0495. The monomer of Fn0495 consists of three subdomains, namely, the N-terminal domain (residues 1-117 and 252-270), the C-terminal domain (residues 273-393), and the loop domain (residues 118-251). Fn0495 shows a unique difference in the charge and structure of the substrate binding pocket compared with homologous proteins. This research found three conserved residues (Cys88, His357, and Cys387) in Fn0495 arranged near a potential substrate binding pocket. In this study, the conformational changes between the covering loop, catalytic cysteine loop, regulatory determinant region, and homologous protein were compared. These results will enhance our understanding of the molecular characteristics and roles of the thiolase family.


  • Organizational Affiliation
    • Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferase
A, B, C, D
402Fusobacterium nucleatum subsp. nucleatum ATCC 25586Mutation(s): 0 
Gene Names: FN0495
EC: 2.3.1.9
UniProt
Find proteins for Q8RG24 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355))
Explore Q8RG24 
Go to UniProtKB:  Q8RG24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RG24
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.243 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.049α = 103.88
b = 78.161β = 93.73
c = 105.327γ = 110.19
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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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: 2023-08-02
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection
  • Version 1.2: 2025-03-19
    Changes: Database references, Structure summary