8P8E | pdb_00008p8e

Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6

• PDB DOI: https://doi.org/10.2210/pdb8P8E/pdb

• Classification: HYDROLASE
• Organism(s): Bacteriophage sp.
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-06-01 Released: 2024-05-08 
• Deposition Author(s): van Raaij, M.J., Sanz-Gaitero, M.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.126 (Depositor), 0.126 (DCC) 

Starting Model: experimental

Literature

Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46.

Sanz-Gaitero, M., De Maesschalck, V., Patel, A., Longin, H., Van Noort, V., Rodriguez-Rubio, L., van Ryne, M., Danis-Wlodarczyk, K., Drulis-Kawa, Z., Mesnage, S., van Raaij, M., Lavigne, R.

(2024) Phage (New Rochelle) 5: 53-62

• PubMed: 39119210 
• DOI: https://doi.org/10.1089/phage.2023.0040
• Primary Citation Related Structures: 
  8P8E


• PubMed Abstract: 
  

  Endolysins are phage-encoded lytic enzymes that degrade bacterial peptidoglycan at the end of phage lytic cycles to release new phage particles. These enzymes are being explored as an alternative to small-molecule antibiotics. The crystal structure of KTN6 Gp46 was determined and compared with a ColabFold model. Cleavage specificity was examined using a peptidoglycan digest and reversed-phase high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS). The structure of KTN6 Gp46 could be determined at 1.4 Å resolution, and key differences in loops of the putative peptidoglycan binding domain were identified in comparison with its closest known homologue, the endolysin of phage SPN1S. Reversed-phase HPLC/MS analysis of the reaction products following peptidoglycan digestion confirmed the muramidase activity of Gp46, consistent with structural predictions. These insights into the structure and function of endolysins further expand the toolbox for endolysin engineering and explore their potential in enzyme-based antibacterial design strategies.

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Organizational Affiliation: 
• Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
Department of Biological Sciences, Munster Technological University, Cork, Ireland.
Laboratory of Gene Technology, KU Leuven, Leuven, Belgium.
School of Biosciences, University of Sheffield, Sheffield, United Kingdom.
Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium.
Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.78 kDa 
• Atom Count: 1,959 
• Modeled Residue Count: 218 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside hydrolase family protein	A [auth AAA]	220	Bacteriophage sp.	Mutation(s): 0  Gene Names: IDBGMNHM_00003
UniProt
Find proteins for A0ACD6BAN9 (Pseudomonas phage Ka2) Explore A0ACD6BAN9  Go to UniProtKB:  A0ACD6BAN9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth EEE], C [auth EaE]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG	D [auth GGG]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.126 (Depositor), 0.126 (DCC) 

Diffraction Data: https://doi.org/10.15785/SBGRID/1103

Diffraction Data: https://doi.org/10.18430/M38P8E

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.796	α = 90
b = 43.201	β = 90
c = 126.181	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-08 
Deposition Author(s): van Raaij, M.J., Sanz-Gaitero, M.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2017-82207-P
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-125597NB-I00

Revision History  

• Version 1.0: 2024-05-08
  Type: Initial release
  
• Version 1.1: 2024-08-21
  Changes: Database references