7QVD | pdb_00007qvd

X-ray structure of the lytic transglycosylase SltB2 from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.195 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.175 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Characterization of Lytic Transglycosylase SltB2 of Pseudomonas aeruginosa.

Miguel-Ruano, V.Batuecas, M.T.Lastochkin, E.Dominguez-Gil, T.Molina, R.Mobashery, S.Hermoso, J.A.

(2025) ACS Omega 10: 48385-48394

  • DOI: https://doi.org/10.1021/acsomega.5c05747
  • Primary Citation of Related Structures:  
    7QVD

  • PubMed Abstract: 

    Lytic transglycosylases (LTs) belong to a family of enzymes that turnover the bacterial cell-wall peptidoglycan through a nonhydrolytic cleavage of the β(1-4) glycosidic bond, generating a hallmark 1,6-anhydromuramyl moiety in the reaction products. LTs are essential for numerous cellular processes, including cell-wall maturation, peptidoglycan recycling, cell division, and the assembly of multiprotein complexes. Their functional diversity underscores their biological significance. Family 3 LTs are distinguished by their EF-hand Ca 2+ -binding motif and are classified into two subfamilies. Subfamily 3B members, including Pseudomonas aeruginosa SltB2, possess a peptidoglycan-binding domain absent in subfamily 3A. In this study, we present the structural characterization of P. aeruginosa SltB2. The high-resolution crystal structure of SltB2 reveals a unique modular architecture shaped by the specific arrangement of its PG-binding domain and distinct differences in the organization of key residues surrounding the catalytic Glu residue compared to other family 3 members. A model of interaction between SltB2 and the peptidoglycan is proposed, which accounts for the enzyme's tolerance to peptide stems and reveals particular features at site +2, due to the unique arrangement of the PG-binding domain, explaining its preferred exolytic activity. Comparative structural analyses of Family 3 LTs provide insights into substrate recognition and enzymatic function, advancing our understanding of bacterial cell-wall remodeling mechanisms.


  • Organizational Affiliation
    • Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Blas Cabrera", Spanish National Research Council (CSIC), Serrano 119, Madrid 28006, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lytic murein transglycosylase380Pseudomonas aeruginosaMutation(s): 0 
Gene Names: IPC1339_08125IPC1598_14895
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.195 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.175 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.966α = 90
b = 42.395β = 95.646
c = 93.579γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPRE2018-085033

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 2.0: 2026-02-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Structure summary