1XOV

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 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


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 Biol 364: 678-689

  • DOI: https://doi.org/10.1016/j.jmb.2006.08.069
  • Primary Citation of 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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

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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 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • 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

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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