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PDBsum entry 1xov

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protein ligands metals links
Hydrolase PDB id
1xov
Jmol
Contents
Protein chain
315 a.a. *
Ligands
SO4
GLU-LYS
TRS
Metals
_ZN
_CL
Waters ×307
* Residue conservation analysis
PDB id:
1xov
Name: Hydrolase
Title: The crystal structure of the listeria monocytogenes bacterio endolysin plypsa
Structure: Ply protein. Chain: a. Synonym: plypsa. Engineered: yes
Source: Listeria phage psa. Organism_taxid: 171618. Gene: ply. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: host: listeria monocytogenes
Resolution:
1.80Å     R-factor:   0.172     R-free:   0.198
Authors: I.P.Korndoerfer,A.Skerra
Key ref:
I.P.Korndörfer et al. (2006). The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls. J Mol Biol, 364, 678-689. PubMed id: 17010991 DOI: 10.1016/j.jmb.2006.08.069
Date:
07-Oct-04     Release date:   18-Oct-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8W5Y8  (Q8W5Y8_9CAUD) -  Ply protein
Seq:
Struc:
314 a.a.
315 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     peptidoglycan catabolic process   1 term 
  Biochemical function     metal ion binding     2 terms  

 

 
DOI no: 10.1016/j.jmb.2006.08.069 J Mol Biol 364:678-689 (2006)
PubMed id: 17010991  
 
 
The crystal structure of the bacteriophage PSA endolysin reveals a unique fold responsible for specific recognition of Listeria cell walls.
I.P.Korndörfer, J.Danzer, M.Schmelcher, M.Zimmer, A.Skerra, M.J.Loessner.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Crystal structure of PlyPSA. The EAD is shown in blue, the linker region in grey, and the CBD in red. The catalytic Zn^2+ is depicted as a yellow sphere. Figure 3. Crystal structure of PlyPSA. The EAD is shown in blue, the linker region in grey, and the CBD in red. The catalytic Zn^2+ is depicted as a yellow sphere.
Figure 8.
Figure 8. Architecture and putative ligand-binding sites of the PlyPSA CBD. (a) Organisation of its two subdomains. Proximal and distal subdomain of the CBD are coloured in orange and red, respectively, except for the structurally swapped strands, which are coloured according to their sequential neighbourhood (see also Figure 1). (b) Superposition of the proximal and distal subdomains (coloured as in (a)). (c) Schematic representation of the ancestral CBD subdomain. (d) Distribution of aromatic side-chains in the CBD and indication of a putative binding site. Residues with uncharged aromatic side-chains are shown as green stick models (backbone coloured as in (a)). (e) Surface representation of the CBD with hydrophobic surface areas coloured in green (as described^53). The white ellipsoid indicates the location of a cleft between the two subdomains that may be suited to bind cell wall associated ligands. Figure 8. Architecture and putative ligand-binding sites of the PlyPSA CBD. (a) Organisation of its two subdomains. Proximal and distal subdomain of the CBD are coloured in orange and red, respectively, except for the structurally swapped strands, which are coloured according to their sequential neighbourhood (see also [3]Figure 1). (b) Superposition of the proximal and distal subdomains (coloured as in (a)). (c) Schematic representation of the ancestral CBD subdomain. (d) Distribution of aromatic side-chains in the CBD and indication of a putative binding site. Residues with uncharged aromatic side-chains are shown as green stick models (backbone coloured as in (a)). (e) Surface representation of the CBD with hydrophobic surface areas coloured in green (as described[4]^53). The white ellipsoid indicates the location of a cleft between the two subdomains that may be suited to bind cell wall associated ligands.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 678-689) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20622130 M.Schmelcher, T.Shabarova, M.R.Eugster, F.Eichenseher, V.S.Tchang, M.Banz, and M.J.Loessner (2010).
Rapid multiplex detection and differentiation of Listeria cells by use of fluorescent phage endolysin cell wall binding domains.
  Appl Environ Microbiol, 76, 5745-5756.  
  20944232 Q.Xu, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, A.Yeh, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1354-1364.
PDB code: 3h41
20300061 T.Uehara, K.R.Parzych, T.Dinh, and T.G.Bernhardt (2010).
Daughter cell separation is controlled by cytokinetic ring-activated cell wall hydrolysis.
  EMBO J, 29, 1412-1422.  
18560152 I.P.Korndörfer, A.Kanitz, J.Danzer, M.Zimmer, M.J.Loessner, and A.Skerra (2008).
Structural analysis of the L-alanoyl-D-glutamate endopeptidase domain of Listeria bacteriophage endolysin Ply500 reveals a new member of the LAS peptidase family.
  Acta Crystallogr D Biol Crystallogr, 64, 644-650.
PDB code: 2vo9
18266855 W.Vollmer, B.Joris, P.Charlier, and S.Foster (2008).
Bacterial peptidoglycan (murein) hydrolases.
  FEMS Microbiol Rev, 32, 259-286.  
17554049 H.Bierne, and P.Cossart (2007).
Listeria monocytogenes surface proteins: from genome predictions to function.
  Microbiol Mol Biol Rev, 71, 377-397.  
17277212 J.W.Kretzer, R.Lehmann, M.Schmelcher, M.Banz, K.P.Kim, C.Korn, and M.J.Loessner (2007).
Use of high-affinity cell wall-binding domains of bacteriophage endolysins for immobilization and separation of bacterial cells.
  Appl Environ Microbiol, 73, 1992-2000.  
17554535 S.Hagens, and M.J.Loessner (2007).
Application of bacteriophages for detection and control of foodborne pathogens.
  Appl Microbiol Biotechnol, 76, 513-519.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.