1XOV

The crystal structure of the listeria monocytogenes bacteriophage PSA endolysin PlyPSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2006.08.069

  • 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 ga ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ply protein
A
326Listeria phage PSAGene Names: ply
Find proteins for Q8W5Y8 (Listeria phage PSA)
Go to UniProtKB:  Q8W5Y8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LYS
Query on LYS

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A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
GLU
Query on GLU

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A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
TRS
Query on TRS

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A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.170 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 90.586α = 90.00
b = 90.586β = 90.00
c = 213.667γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHARPphasing
CCP4data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-18
    Type: Initial release
  • Version 1.1: 2008-04-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance