9KBQ | pdb_00009kbq

Crystal structure of PHAb10, a peptidoglycan hydrolase with thermal stability and broad-spectrum

  • Classification: LYASE
  • Organism(s): Acinetobacter baumannii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-10-31 Released: 2024-11-27 
  • Deposition Author(s): Hu, F.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Dimer-monomer transition defines a hyper-thermostable peptidoglycan hydrolase mined from bacterial proteome by lysin-derived antimicrobial peptide-primed screening.

Zhang, L.Hu, F.Zhao, Z.Li, X.Zhong, M.He, J.Yao, F.Zhang, X.Mao, Y.Wei, H.He, J.Yang, H.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.98266
  • Primary Citation of Related Structures:  
    9KBQ, 9KBS, 9KBT

  • PubMed Abstract: 

    Phage-derived peptidoglycan hydrolases (i.e. lysins) are considered promising alternatives to conventional antibiotics due to their direct peptidoglycan degradation activity and low risk of resistance development. The discovery of these enzymes is often hampered by the limited availability of phage genomes. Herein, we report a new strategy to mine active peptidoglycan hydrolases from bacterial proteomes by lysin-derived antimicrobial peptide-primed screening. As a proof-of-concept, five p eptidoglycan h ydrolases from the A cinetobacter b aumannii proteome (PHAb7-PHAb11) were identified using PlyF307 lysin-derived peptide as a template. Among them, PHAb10 and PHAb11 showed potent bactericidal activity against multiple pathogens even after treatment at 100°C for 1 hr, while the other three were thermosensitive. We solved the crystal structures of PHAb8, PHAb10, and PHAb11 and unveiled that hyper-thermostable PHAb10 underwent a unique folding-refolding thermodynamic scheme mediated by a dimer-monomer transition, while thermosensitive PHAb8 formed a monomer. Two mouse models of bacterial infection further demonstrated the safety and efficacy of PHAb10. In conclusion, our antimicrobial peptide-primed strategy provides new clues for the discovery of promising antimicrobial drugs.


  • Organizational Affiliation
    • National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme
A, B
149Acinetobacter baumanniiMutation(s): 0 
Gene Names: FJU42_09780
EC: 3.2.1.17
UniProt
Find proteins for A0A009PZ93 (Acinetobacter baumannii 625974)
Explore A0A009PZ93 
Go to UniProtKB:  A0A009PZ93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A009PZ93
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.215 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.86α = 90
b = 73.77β = 93.02
c = 78.62γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
xia2data scaling
PHASESphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-11-27 
  • Deposition Author(s): Hu, F.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81802001

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 1.2: 2025-06-18
    Changes: Database references