9KZ1 | pdb_00009kz1

Crystal structure of PlySb from a chimeolysin ClyR

• PDB DOI: https://doi.org/10.2210/pdb9KZ1/pdb

• Classification: LIGASE
• Organism(s): Streptococcus phage phiLP081102
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-09 Released: 2025-10-22 
• Deposition Author(s): Hu, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.201 (Depositor), 0.197 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Domain Interactions in a Chimeric Dual-domain Lysin Lead to Broad Bactericidal Activity.

Hu, F., Zhang, X., Gong, Z., Wu, P., Zhao, Q., Zheng, Y., Gao, H., Chou, S.H., Li, X., Zhong, M., Zhao, Z., Shi, N., Wei, H., He, J., Yang, H.

(2025) J Mol Biology 437: 169373-169373

• PubMed: 40769489 
• DOI: https://doi.org/10.1016/j.jmb.2025.169373
• Primary Citation of Related Structures:  
  9KZ1


• PubMed Abstract: 
  

  Phage-derived lysins represent a novel, non-traditional therapeutic agent against multidrug-resistant bacteria. However, engineering lysins with broad host range remain poorly addressed. Previously, we reported that the chimeric lysin ClyR, which harbors the CHAP catalytic domain of PlyC lysin (PlyCAC) and the SH3b cell-wall binding domain of PlySs2 lysin (PlySb), exhibits an expanded host range. However, the mechanism by which ClyR exhibits expanded bactericidal activity is still not fully understood. Since the structure of PlyCAC is publicly available (PDB code: 4F88), here, we first solve the crystal structure of PlySb using X-ray diffraction, and then use various biophysical methods, such as X-ray diffraction, cross-linking coupled mass spectrometry (CXMS), and small-angle X-ray scattering (SAXS) to analyze the potential full-length structures of ClyR. Our results demonstrate that ClyR exhibits a dynamic conformation supported by multiple inter-domain interactions between the two constituent domains. Mutagenesis and biochemical analysis further support the notion that these inter-domain interactions may modulate the bactericidal activity of ClyR. Altogether, our findings provide novel insights into the action mechanism of ClyR and a better understanding of how inter-domain interactions influence the host range of chimeric lysins.

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Organizational Affiliation: 
• Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350002, China; State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China.
State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China.
CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350002, China.
State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.
State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
National Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China. Electronic address: [e-mail].
State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Hubei Jiangxia Laboratory, Wuhan 430200, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 10.62 kDa 
• Atom Count: 784 
• Modeled Residue Count: 85 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase	A	99	Streptococcus phage phiLP081102	Mutation(s): 0  EC: 3.5.1.28

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.201 (Depositor), 0.197 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.41	α = 90
b = 75.785	β = 90
c = 38.887	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Hu, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81802001

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release