7PL5

Crystal structure of choline-binding module (R1-R9) of LytB from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular basis of the final step of cell division in Streptococcus pneumoniae.

Martinez-Caballero, S.Freton, C.Molina, R.Bartual, S.G.Gueguen-Chaignon, V.Mercy, C.Gago, F.Mahasenan, K.V.Munoz, I.G.Lee, M.Hesek, D.Mobashery, S.Hermoso, J.A.Grangeasse, C.

(2023) Cell Rep 42: 112756-112756

  • DOI: https://doi.org/10.1016/j.celrep.2023.112756
  • Primary Citation of Related Structures:  
    7PJ3, 7PJ4, 7PJ5, 7PJ6, 7PL2, 7PL3, 7PL5, 7POD

  • PubMed Abstract: 

    Bacterial cell-wall hydrolases must be tightly regulated during bacterial cell division to prevent aberrant cell lysis and to allow final separation of viable daughter cells. In a multidisciplinary work, we disclose the molecular dialogue between the cell-wall hydrolase LytB, wall teichoic acids, and the eukaryotic-like protein kinase StkP in Streptococcus pneumoniae. After characterizing the peptidoglycan recognition mode by the catalytic domain of LytB, we further demonstrate that LytB possesses a modular organization allowing the specific binding to wall teichoic acids and to the protein kinase StkP. Structural and cellular studies notably reveal that the temporal and spatial localization of LytB is governed by the interaction between specific modules of LytB and the final PASTA domain of StkP. Our data collectively provide a comprehensive understanding of how LytB performs final separation of daughter cells and highlights the regulatory role of eukaryotic-like kinases on lytic machineries in the last step of cell division in streptococci.


  • Organizational Affiliation

    Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative endo-beta-N-acetylglucosaminidaseA [auth AAA],
B [auth BBB]
185Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: lytBspr0867
EC: 3.2.1.96
UniProt
Find proteins for P59206 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore P59206 
Go to UniProtKB:  P59206
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59206
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
M [auth BBB]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CHT
Query on CHT

Download Ideal Coordinates CCD File 
C [auth AAA]
D [auth AAA]
E [auth AAA]
F [auth AAA]
G [auth AAA]
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
K [auth BBB],
L [auth BBB],
N [auth BBB],
O [auth BBB],
P [auth BBB],
Q [auth BBB]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth AAA],
J [auth AAA],
R [auth BBB],
S [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.299α = 90
b = 96.143β = 100.966
c = 49.096γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MoRDaphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Structure summary
  • Version 1.2: 2023-07-12
    Changes: Database references
  • Version 1.3: 2023-07-19
    Changes: Database references, Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Refinement description