1XJT

Crystal structure of active form of P1 phage endolysin Lyz


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 

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:  

  • 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
191Escherichia phage P1Mutation(s): 0 
Gene Names: 17 (lysa, lyz)
EC: 3.2.1.17
Find proteins for Q37875 (Escherichia phage P1)
Go to UniProtKB:  Q37875
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.208 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.871α = 90.00
b = 66.871β = 90.00
c = 166.796γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
Adxvdata processing
SHARPphasing
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

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: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description