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Hydrolase PDB id
1wra
Jmol
Contents
Protein chains
305 a.a. *
Ligands
_PC ×2
MPD ×11
Metals
_FE ×4
_CA ×4
Waters ×363
* Residue conservation analysis
PDB id:
1wra
Name: Hydrolase
Title: Crystal structure of phosphorylcholine esterase domain of the virulence factor choline binding protein e from streptococcus pneumoniae
Structure: Teichoic acid phosphorylcholine esterase/choline binding protein e (cbpe). Chain: a, b. Fragment: catalytic domain. Engineered: yes
Source: Streptococcus pneumoniae r6. Organism_taxid: 171101. Strain: atcc baa-255 / r6. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.00Å     R-factor:   0.176     R-free:   0.204
Authors: G.Garau,O.Dideberg
Key ref:
G.Garau et al. (2005). Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily. J Biol Chem, 280, 28591-28600. PubMed id: 15908436 DOI: 10.1074/jbc.M502744200
Date:
13-Oct-04     Release date:   31-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8DQ62  (Q8DQ62_STRR6) -  Teichoic acid phosphorylcholine esterase/choline binding protein E (CbpE)
Seq:
Struc: 		 
Seq:
Struc: 		627 a.a.
306 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     hydrolase activity     1 term  

 

 
DOI no: 10.1074/jbc.M502744200 J Biol Chem 280:28591-28600 (2005)
PubMed id: 15908436  
 
 
Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily.
G.Garau, D.Lemaire, T.Vernet, O.Dideberg, A.M.Di Guilmi.
 
  ABSTRACT  
 
Streptococcus pneumoniae is the worldwide leading cause of deaths from invasive infections such as pneumoniae, sepsis, and meningitidis in children and the elderly. Nasopharyngeal colonization, which plays a key role in the development of pneumococcal disease, is highly dependent on a family of surface-exposed proteins, the choline-binding proteins (CBPs). Here we report the crystal structure of phosphorylcholine esterase (Pce), the catalytic domain of choline-binding protein E (CBPE), which has been shown to be crucial for host/pathogen interaction processes. The unexpected features of the Pce active site reveal that this enzyme is unique among the large family of hydrolases harboring the metallo-beta-lactamase fold. The orientation and calcium stabilization features of an elongated loop, which lies on top of the active site, suggest that the cleft may be rearranged. Furthermore, the structure of Pce complexed with phosphorylcholine, together with the characterization of the enzymatic role played by two iron ions located in the active site allow us to propose a reaction mechanism reminiscent of that of purple acid phosphatase. This mechanism is supported by site-directed mutagenesis experiments. Finally, the interactions of the choline binding domain and the Pce region of CBPE with chains of teichoic acids have been modeled. The ensemble of our biochemical and structural results provide an initial understanding of the function of CBPE.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. Structural architecture of the Pce active site. A, elongated loop. With respect to the orientation of the Pce protein in Fig. 1B, the elongated loop is viewed 90 °C from the left side. The backbone and the lateral chains of residues of the loop are colored in orange, whereas residues from the helical structural elements of Pce are shown in blue. Both Ca^2+ ions appear as gray balls. B, enzymatic cavity. With respect to the orientation of the Pce protein in Fig. 1B, the enzymatic cavity is viewed 90 °C from the right side. Important amino acids and PCho are represented in ball-and-stick, iron and calcium ions as purple and gray spheres, respectively. 		Figure 4.
FIG. 4. Schematic diagram of the interactions and the interatomic distances in the binuclear active site of Pce.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 28591-28600) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21048085 K.Hashimoto, and A.R.Panchenko (2010).
Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states.
  Proc Natl Acad Sci U S A, 107, 20352-20357.  
20385411 V.A.Campos-Bermudez, J.Morán-Barrio, A.J.Costa-Filho, and A.J.Vila (2010).
Metal-dependent inhibition of glyoxalase II: a possible mechanism to regulate the enzyme activity.
  J Inorg Biochem, 104, 726-731.  
20040078 M.Lescat, C.Hoede, O.Clermont, L.Garry, P.Darlu, P.Tuffery, E.Denamur, and B.Picard (2009).
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species.
  BMC Microbiol, 9, 273.  
18725422 C.Attali, C.Durmort, T.Vernet, and A.M.Di Guilmi (2008).
The interaction of Streptococcus pneumoniae with plasmin mediates transmigration across endothelial and epithelial monolayers by intercellular junction cleavage.
  Infect Immun, 76, 5350-5356.  
18070889 C.Attali, C.Frolet, C.Durmort, J.Offant, T.Vernet, and A.M.Di Guilmi (2008).
Streptococcus pneumoniae choline-binding protein E interaction with plasminogen/plasmin stimulates migration across the extracellular matrix.
  Infect Immun, 76, 466-476.  
18627129 D.Liu, J.Momb, P.W.Thomas, A.Moulin, G.A.Petsko, W.Fast, and D.Ringe (2008).
Mechanism of the quorum-quenching lactonase (AiiA) from Bacillus thuringiensis. 1. Product-bound structures.
  Biochemistry, 47, 7706-7714.
PDB codes: 3dha 3dhb 3dhc
16916792 A.Minagawa, H.Takaku, R.Ishii, M.Takagi, S.Yokoyama, and M.Nashimoto (2006).
Identification by Mn2+ rescue of two residues essential for the proton transfer of tRNase Z catalysis.
  Nucleic Acids Res, 34, 3811-3818.  
16684886 G.Hagelueken, T.M.Adams, L.Wiehlmann, U.Widow, H.Kolmar, B.Tümmler, D.W.Heinz, and W.D.Schubert (2006).
The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases.
  Proc Natl Acad Sci U S A, 103, 7631-7636.
PDB codes: 2cfu 2cfz 2cg2 2cg3
  16820691 N.G.Paterson, A.Riboldi-Tunicliffe, T.J.Mitchell, and N.W.Isaacs (2006).
Overexpression, purification and crystallization of a choline-binding protein CbpI from Streptococcus pneumoniae.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 672-675.  
16338163 S.Hammerschmidt (2006).
Adherence molecules of pathogenic pneumococci.
  Curr Opin Microbiol, 9, 12-20.  
16336119 A.Vogel, O.Schilling, B.Späth, and A.Marchfelder (2005).
The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties.
  Biol Chem, 386, 1253-1264.  
16260756 L.Lagartera, A.González, J.A.Hermoso, J.L.Saíz, P.García, J.L.García, and M.Menéndez (2005).
Pneumococcal phosphorylcholine esterase, Pce, contains a metal binuclear center that is essential for substrate binding and catalysis.
  Protein Sci, 14, 3013-3024.  
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 codes are shown on the right.