1XJU

Crystal structure of secreted inactive form of P1 phage endolysin Lyz


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Disulfide isomerization after membrane release of its SAR domain activates P1 lysozyme.

Xu, M.Arulandu, A.Struck, D.K.Swanson, S.Sacchettini, J.C.Young, R.

(2005) Science 307: 113-117

  • DOI: 10.1126/science.1105143
  • Primary Citation of Related Structures:  1XJT

  • PubMed Abstract: 
  • The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-dis ...

    The P1 lysozyme Lyz is secreted to the periplasm of Escherichia coli and accumulates in an inactive membrane-tethered form. Genetic and biochemical experiments show that, when released from the bilayer, Lyz is activated by an intramolecular thiol-disulfide isomerization, which requires a cysteine in its N-terminal SAR (signal-arrest-release) domain. Crystal structures confirm the alternative disulfide linkages in the two forms of Lyz and reveal dramatic conformational differences in the catalytic domain. Thus, the exported P1 endolysin is kept inactive by three levels of control-topological, conformational, and covalent-until its release from the membrane is triggered by the P1 holin.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B
163Enterobacteria phage P1Gene Names: 17 (lysa, lyz)
EC: 3.2.1.17
Find proteins for Q37875 (Enterobacteria phage P1)
Go to UniProtKB:  Q37875
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.133 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.349α = 90.00
b = 59.786β = 102.51
c = 76.228γ = 90.00
Software Package:
Software NamePurpose
Adxvdata processing
EPMRphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description