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PDBsum entry 1oba

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Hydrolase PDB id
1oba
Jmol
Contents
Protein chain
338 a.a. *
Ligands
CHT ×2
Waters ×257
* Residue conservation analysis
PDB id:
1oba
Name: Hydrolase
Title: Multimodular pneumococcal cell wall endolysin from phage cp-1 complexed with choline
Structure: Lysozyme. Chain: a. Synonym: murein hydrolase, endolysin, muramidase, cp-1 lysin. Engineered: yes
Source: Bacteriophage cp-1. Organism_taxid: 10747. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.45Å     R-factor:   0.205     R-free:   0.264
Authors: J.A.Hermoso,B.Monterroso,A.Albert,P.Garcia,M.Menendez, M.Martinez-Ripoll,J.L.Garcia
Key ref:
J.A.Hermoso et al. (2003). Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1. Structure, 11, 1239-1249. PubMed id: 14527392 DOI: 10.1016/j.str.2003.09.005
Date:
29-Jan-03     Release date:   17-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15057  (LYS_BPCP1) -  Lysozyme
Seq:
Struc:
339 a.a.
338 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1016/j.str.2003.09.005 Structure 11:1239-1249 (2003)
PubMed id: 14527392  
 
 
Structural basis for selective recognition of pneumococcal cell wall by modular endolysin from phage Cp-1.
J.A.Hermoso, B.Monterroso, A.Albert, B.Galán, O.Ahrazem, P.García, M.Martínez-Ripoll, J.L.García, M.Menéndez.
 
  ABSTRACT  
 
Pneumococcal bacteriophage-encoded lysins are modular choline binding proteins that have been shown to act as enzymatic antimicrobial agents (enzybiotics) against streptococcal infections. Here we present the crystal structures of the free and choline bound states of the Cpl-1 lysin, encoded by the pneumococcal phage Cp-1. While the catalytic module displays an irregular (beta/alpha)(5)beta(3) barrel, the cell wall-anchoring module is formed by six similar choline binding repeats (ChBrs), arranged into two different structural regions: a left-handed superhelical domain configuring two choline binding sites, and a beta sheet domain that contributes in bringing together the whole structure. Crystallographic and site-directed mutagenesis studies allow us to propose a general catalytic mechanism for the whole glycoside hydrolase family 25. Our work provides the first complete structure of a member of the large family of choline binding proteins and reveals that ChBrs are versatile elements able to tune the evolution and specificity of the pneumococcal surface proteins.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of Modular Cpl-1 Endolysin(A) Stereo representation of Cpl-1 structure with domains colored differently. Catalytic N-terminal, green; linker, orange; CI domain, cyan; CII domain, magenta. Choline molecules are drawn in a ball-and-stick representation.(B) Topology diagram of Cpl-1. Domains are color-coded as in (A) with the antiparallel b8 strand of the catalytic module highlighted in orange. In the choline binding model, the different ChBrs (p1-p6) are labeled.(C) Comparison of the amino acid sequence of the ChBrs and the C-terminal tail in Cpl-1. The structural domain, the repeat number, and their corresponding amino acids are shown on the left. Residues in b strand conformation are shadowed in yellow. Conserved amino acids among the repeats appear in black boxes. Its consensus sequence (>=50%) is shown at the bottom. Upper case indicates 100% conservation.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1239-1249) copyright 2003.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20963614 B.S.Seal, D.E.Fouts, M.Simmons, J.K.Garrish, R.L.Kuntz, R.Woolsey, K.M.Schegg, A.M.Kropinski, H.W.Ackermann, and G.R.Siragusa (2011).
Clostridium perfringens bacteriophages ΦCP39O and ΦCP26F: genomic organization and proteomic analysis of the virions.
  Arch Virol, 156, 25-35.  
21085950 J.E.Schmitz, M.C.Ossiprandi, K.R.Rumah, and V.A.Fischetti (2011).
Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens.
  Appl Microbiol Biotechnol, 89, 1783-1795.  
20400948 I.Pérez-Dorado, A.González, M.Morales, R.Sanles, W.Striker, W.Vollmer, S.Mobashery, J.L.García, M.Martínez-Ripoll, P.García, and J.A.Hermoso (2010).
Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC.
  Nat Struct Mol Biol, 17, 576-581.
PDB codes: 2ww5 2wwc 2wwd
20803062 J.R.van der Ploeg (2010).
Genome sequence of the temperate bacteriophage PH10 from Streptococcus oralis.
  Virus Genes, 41, 450-458.  
19165143 R.Molina, A.González, M.Stelter, I.Pérez-Dorado, R.Kahn, M.Morales, S.Campuzano, N.E.Campillo, S.Mobashery, J.L.García, P.García, and J.A.Hermoso (2009).
Crystal structure of CbpF, a bifunctional choline-binding protein and autolysis regulator from Streptococcus pneumoniae.
  EMBO Rep, 10, 246-251.
PDB codes: 2v04 2vyu
19633119 S.Campuzano, B.Serra, D.Llull, J.L.García, and P.García (2009).
Cloning, expression, and characterization of a peculiar choline-binding beta-galactosidase from Streptococcus mitis.
  Appl Environ Microbiol, 75, 5972-5980.  
18667432 B.Monterroso, J.L.Sáiz, P.García, J.L.García, and M.Menéndez (2008).
Insights into the Structure-Function Relationships of Pneumococcal Cell Wall Lysozymes, LytC and Cpl-1.
  J Biol Chem, 283, 28618-28628.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18824123 V.A.Fischetti (2008).
Bacteriophage lysins as effective antibacterials.
  Curr Opin Microbiol, 11, 393-400.  
17229144 B.Maestro, A.González, P.García, and J.M.Sanz (2007).
Inhibition of pneumococcal choline-binding proteins and cell growth by esters of bicyclic amines.
  FEBS J, 274, 364-376.  
17353242 D.Llull, L.Rivas, and E.García (2007).
In vitro bactericidal activity of the antiprotozoal drug miltefosine against Streptococcus pneumoniae and other pathogenic streptococci.
  Antimicrob Agents Chemother, 51, 1844-1848.  
17581815 I.Pérez-Dorado, N.E.Campillo, B.Monterroso, D.Hesek, M.Lee, J.A.Páez, P.García, M.Martínez-Ripoll, J.L.García, S.Mobashery, M.Menéndez, and J.A.Hermoso (2007).
Elucidation of the molecular recognition of bacterial cell wall by modular pneumococcal phage endolysin CPL-1.
  J Biol Chem, 282, 24990-24999.
PDB codes: 2ixu 2ixv 2j8f 2j8g
17937816 J.Dundas, T.A.Binkowski, B.DasGupta, and J.Liang (2007).
Topology independent protein structural alignment.
  BMC Bioinformatics, 8, 388.  
17711456 J.R.van der Ploeg (2007).
Genome sequence of Streptococcus mutans bacteriophage M102.
  FEMS Microbiol Lett, 275, 130-138.  
17439951 P.Romero, R.López, and E.García (2007).
Key role of amino acid residues in the dimerization and catalytic activation of the autolysin LytA, an important virulence factor in Streptococcus pneumoniae.
  J Biol Chem, 282, 17729-17737.  
17518365 P.Veiga-Crespo, J.M.Ageitos, M.Poza, and T.G.Villa (2007).
Enzybiotics: a look to the future, recalling the past.
  J Pharm Sci, 96, 1917-1924.  
17697255 Y.Briers, G.Volckaert, A.Cornelissen, S.Lagaert, C.W.Michiels, K.Hertveldt, and R.Lavigne (2007).
Muralytic activity and modular structure of the endolysins of Pseudomonas aeruginosa bacteriophages phiKZ and EL.
  Mol Microbiol, 65, 1334-1344.  
15908436 G.Garau, D.Lemaire, T.Vernet, O.Dideberg, and A.M.Di Guilmi (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.
PDB codes: 1wra 2v05
15895092 J.A.Hermoso, L.Lagartera, A.González, M.Stelter, P.García, M.Martínez-Ripoll, J.L.García, and M.Menéndez (2005).
Insights into pneumococcal pathogenesis from the crystal structure of the modular teichoic acid phosphorylcholine esterase Pce.
  Nat Struct Mol Biol, 12, 533-538.
PDB code: 2bib
15979390 M.J.Loessner (2005).
Bacteriophage endolysins--current state of research and applications.
  Curr Opin Microbiol, 8, 480-487.  
16332865 M.Moscoso, V.Obregón, R.López, J.L.García, and E.García (2005).
Allelic variation of polymorphic locus lytB, encoding a choline-binding protein, from streptococci of the mitis group.
  Appl Environ Microbiol, 71, 8706-8713.  
15980371 M.Takác, and U.Bläsi (2005).
Phage P68 virion-associated protein 17 displays activity against clinical isolates of Staphylococcus aureus.
  Antimicrob Agents Chemother, 49, 2934-2940.  
16125935 V.A.Fischetti (2005).
Bacteriophage lytic enzymes: novel anti-infectives.
  Trends Microbiol, 13, 491-496.  
15247237 J.Varea, B.Monterroso, J.L.Sáiz, C.López-Zumel, J.L.García, J.Laynez, P.García, and M.Menéndez (2004).
Structural and thermodynamic characterization of Pal, a phage natural chimeric lysin active against pneumococci.
  J Biol Chem, 279, 43697-43707.  
15576771 P.Romero, R.López, and E.García (2004).
Characterization of LytA-like N-acetylmuramoyl-L-alanine amidases from two new Streptococcus mitis bacteriophages provides insights into the properties of the major pneumococcal autolysin.
  J Bacteriol, 186, 8229-8239.  
15539074 R.López, and E.García (2004).
Recent trends on the molecular biology of pneumococcal capsules, lytic enzymes, and bacteriophage.
  FEMS Microbiol Rev, 28, 553-580.  
14604518 G.Anderluh, and P.Macek (2003).
Dissecting the actinoporin pore-forming mechanism.
  Structure, 11, 1312-1313.  
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.