Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group P4332)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Structural and biochemical analyses of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis.

Na, H.W.Namgung, B.Song, W.S.Yoon, S.I.

(2019) Biochem Biophys Res Commun 519: 35-40

  • DOI: https://doi.org/10.1016/j.bbrc.2019.08.106
  • Primary Citation of Related Structures:  
    6KNS, 6KNT

  • PubMed Abstract: 

    Metallo-β-lactamase (MBL) fold proteins play critical roles in diverse biological processes, such as DNA repair, RNA processing, detoxification, and metabolism. Although MBL fold proteins share a metal-bound αββα structure, they are highly heterogeneous in metal type, metal coordination, and oligomerization and exhibit different catalytic functions. Bacillus subtilis contains the yhfI gene, which is predicted to encode an MBL fold protein. To reveal the structural and functional features of YhfI, we determined two crystal structures of YhfI and biochemically characterized the catalytic activity of YhfI. YhfI forms an α-helix-decorated β-sandwich structure and assembles into a dimer using highly conserved residues. Each YhfI chain simultaneously interacts with two metal ions, which are coordinated by histidine and aspartate residues that are strictly conserved in YhfI orthologs. A comparative analysis of YhfI and its homologous structures suggests that YhfI would function as a phosphodiesterase. Indeed, YhfI drove the phosphodiesterase reaction and showed high catalytic activity at pH 8.0-9.5 in the presence of manganese. Moreover, we propose that the active site of YhfI is located at a metal-containing pocket generated between the two subunits of a YhfI dimer.

  • Organizational Affiliation

    Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative metal-dependent hydrolase
A, B, C, D
250Bacillus subtilisMutation(s): 0 
Gene Names: yhfI
Find proteins for E0TYN8 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23))
Explore E0TYN8 
Go to UniProtKB:  E0TYN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0TYN8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.754α = 90
b = 202.754β = 90
c = 202.754γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description