4CGK | pdb_00004cgk

Crystal structure of the essential protein PcsB from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4CGK

This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Pcsb-Mediated Cell Separation in Streptococcus Pneumoniae.

Bartual, S.G.Straume, D.Stamsas, G.A.Munoz, I.G.Alfonso, C.Martinez-Ripoll, M.Havarstein, L.S.Hermoso, J.A.

(2014) Nat Commun 5: 3842

  • DOI: https://doi.org/10.1038/ncomms4842
  • Primary Citation Related Structures: 
    4CGK

  • PubMed Abstract: 

    Separation of daughter cells during bacterial cell division requires splitting of the septal cross wall by peptidoglycan hydrolases. In Streptococcus pneumoniae, PcsB is predicted to perform this operation. Recent evidence shows that PcsB is recruited to the septum by the transmembrane FtsEX complex, and that this complex is required for cell division. However, PcsB lacks detectable catalytic activity in vitro, and while it has been proposed that FtsEX activates PcsB, evidence for this is lacking. Here we demonstrate that PcsB has muralytic activity, and report the crystal structure of full-length PcsB. The protein adopts a dimeric structure in which the V-shaped coiled-coil (CC) domain of each monomer acts as a pair of molecular tweezers locking the catalytic domain of each dimeric partner in an inactive configuration. This suggests that the release of the catalytic domains likely requires an ATP-driven conformational change in the FtsEX complex, conveyed towards the catalytic domains through coordinated movements of the CC domain.


  • Organizational Affiliation
    • 1] Department of Crystallography and Structural Biology, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain [2].

Macromolecule Content 

  • Total Structure Weight: 84.1 kDa 
  • Atom Count: 5,709 
  • Modeled Residue Count: 699 
  • Deposited Residue Count: 784 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SECRETED 45 KDA PROTEIN
A, B
392Streptococcus pneumoniae D39Mutation(s): 0 
EC: 3.2.1
UniProt
Find proteins for A0A0H2ZQ76 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466))
Explore A0A0H2ZQ76 
Go to UniProtKB:  A0A0H2ZQ76
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZQ76
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
M [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
L [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.272 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.815α = 90
b = 125.815β = 90
c = 126.637γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other