1XOV | pdb_00001xov

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1XOV

This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls

Korndoerfer, I.P.Danzer, J.Schmelcher, M.Zimmer, M.Skerra, A.Loessner, M.J.

(2006) J Mol Biology 364: 678-689

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.069
  • Primary Citation Related Structures: 
    1XOV

  • PubMed Abstract: 

    Bacteriophage murein hydrolases exhibit high specificity towards the cell walls of their host bacteria. This specificity is mostly provided by a structurally well defined cell wall-binding domain that attaches the enzyme to its solid substrate. To gain deeper insight into this mechanism we have crystallized the complete 314 amino acid endolysin from the temperate Listeria monocytogenes phage PSA. The crystal structure of PlyPSA was determined by single wavelength anomalous dispersion methods and refined to 1.8 A resolution. The two functional domains of the polypeptide, providing cell wall-binding and enzymatic activities, can be clearly distinguished and are connected via a linker segment of six amino acid residues. The core of the N-acetylmuramoyl-L-alanine amidase moiety is formed by a twisted, six-stranded beta-sheet flanked by six helices. Although the catalytic domain is unique among the known Listeria phage endolysins, its structure is highly similar to known phosphorylase/hydrolase-like alpha/beta-proteins, including an autolysin amidase from Paenibacillus polymyxa. In contrast, the C-terminal domain of PlyPSA features a novel fold, comprising two copies of a beta-barrel-like motif, which are held together by means of swapped beta-strands. The architecture of the enzyme with its two separate domains explains its unique substrate recognition properties and also provides insight into the lytic mechanisms of related Listeria phage endolysins, a class of enzymes that bear biotechnological potential.


  • Organizational Affiliation
    • Technische Universität München, Lehrstuhl für Biologische Chemie, An der Saatzucht 5, D-85350 Freising, Germany. ipk@crystax.com

Macromolecule Content 

  • Total Structure Weight: 37.26 kDa 
  • Atom Count: 2,828 
  • Modeled Residue Count: 315 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ply protein326Listeria phage PSAMutation(s): 0 
Gene Names: ply
EC: 3.5.1.28
UniProt
Find proteins for Q8W5Y8 (Listeria phage PSA)
Explore Q8W5Y8 
Go to UniProtKB:  Q8W5Y8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8W5Y8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS

Query on LYS



Download:Ideal Coordinates CCD File
F [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
GLU

Query on GLU



Download:Ideal Coordinates CCD File
E [auth A]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.586α = 90
b = 90.586β = 90
c = 213.667γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2024-01-03
    Changes: Data collection, Database references, Derived calculations