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PDBsum entry 2bsd

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protein Protein-protein interface(s) links
Receptor PDB id
2bsd
Jmol
Contents
Protein chains
254 a.a. *
Waters ×215
* Residue conservation analysis
PDB id:
2bsd
Name: Receptor
Title: Structure of lactococcal bacteriophage p2 receptor binding protein
Structure: Receptor binding protein. Chain: a, b, c. Engineered: yes
Source: Enterobacteria phage p2. Organism_taxid: 10679. Strain: lm0230. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.221     R-free:   0.252
Authors: S.Spinelli,A.Desmyter,C.T.Verrips,H.J.W.Dehaard,S.Moineau, C.Cambillau
Key ref:
S.Spinelli et al. (2006). Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses. Nat Struct Mol Biol, 13, 85-89. PubMed id: 16327804 DOI: 10.1038/nsmb1029
Date:
20-May-05     Release date:   02-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q71AW2  (Q71AW2_9CAUD) -  Putative receptor binding protein
Seq:
Struc:
264 a.a.
254 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell adhesion   3 terms 

 

 
DOI no: 10.1038/nsmb1029 Nat Struct Mol Biol 13:85-89 (2006)
PubMed id: 16327804  
 
 
Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses.
S.Spinelli, A.Desmyter, C.T.Verrips, H.J.de Haard, S.Moineau, C.Cambillau.
 
  ABSTRACT  
 
Lactococcus lactis is a Gram-positive bacterium used extensively by the dairy industry for the manufacture of fermented milk products. The double-stranded DNA bacteriophage p2 infects specific L. lactis strains using a receptor-binding protein (RBP) located at the tip of its noncontractile tail. We have solved the crystal structure of phage p2 RBP, a homotrimeric protein composed of three domains: the shoulders, a beta-sandwich attached to the phage; the neck, an interlaced beta-prism; and the receptor-recognition head, a seven-stranded beta-barrel. We used the complex of RBP with a neutralizing llama VHH domain to identify the receptor-binding site. Structural similarity between the recognition-head domain of phage p2 and those of adenoviruses and reoviruses, which invade mammalian cells, suggests that these viruses, despite evolutionary distant targets, lack of sequence similarity and the different chemical nature of their genomes (DNA versus RNA), might have a common ancestral gene.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Individual domains of the receptor-binding protein from phage p2. (a) The shoulder domain, with a rainbow color gradient from the N-terminus (blue) to the C-terminus (red). -strands are numbered sequentially 1-8. Dashed line indicates the absence of residues 10-18 in the electron density map. (b) The neck -prism domain formed by the interlaced assembly of three segments within positions 142-163. The three faces of the -prism are identified by the letters A, B and C; the strands in each subunit are numbered 1-4. (c) The head domain with a rainbow color gradient from the N-terminus (blue) to the C-terminus (red). -strands are numbered sequentially 1-7. The view is rotated 90 from that in b. (d) Common double Greek-key topology shared by phage p2, adenovirus and reovirus RBPs. The fourth strand of the Greek-key motif is disordered in phage p2. (e) Sequence alignment of the RBPs from phages p2, sk1 and bIL170. The secondary structure of phage p2 RBP is indicated above the alignments and -strands are colored red, green or blue to denote their location in the shoulders, neck or head, respectively (alignment made by MULTALIN (http://prodes.toulouse.inra.fr/multalin/multalin.html)).
Figure 3.
Figure 3. The complex of the phage p2 RBP head with VHH5. (a) The RBP-VHH5 complex. The three head domains, the only parts of RBP observed in the structure of the complex, are in gray. The three VHH5s are colored red, green and blue. (b) Views of the surface of the RBP-head trimer that interacts with VHH5 (white). Inset, spheres representation of the RBP-head residues interacting with VHH5. Residues labeled with and without asterisks are from different monomers. (c) VHH5 CDR1 (red), CDR2 (green) and CDR3 (blue). The surface interacting with the RBP is circled by a white line encompassing part of the CDRs.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 85-89) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20506290 D.Veesler, S.Blangy, S.Spinelli, P.Tavares, V.Campanacci, and C.Cambillau (2010).
Crystal structure of Bacillus subtilis SPP1 phage gp22 shares fold similarity with a domain of lactococcal phage p2 RBP.
  Protein Sci, 19, 1439-1443.
PDB code: 2xc8
20351260 G.Sciara, C.Bebeacua, P.Bron, D.Tremblay, M.Ortiz-Lombardia, J.Lichière, M.van Heel, V.Campanacci, S.Moineau, and C.Cambillau (2010).
Structure of lactococcal phage p2 baseplate and its mechanism of activation.
  Proc Natl Acad Sci U S A, 107, 6852-6857.
PDB codes: 2wzp 2x53 2x54 2x5a
  21129200 P.G.Leiman, F.Arisaka, M.J.van Raaij, V.A.Kostyuchenko, A.A.Aksyuk, S.Kanamaru, and M.G.Rossmann (2010).
Morphogenesis of the T4 tail and tail fibers.
  Virol J, 7, 355.  
19740746 D.Veesler, B.Dreier, S.Blangy, J.Lichière, D.Tremblay, S.Moineau, S.Spinelli, M.Tegoni, A.Plückthun, V.Campanacci, and C.Cambillau (2009).
Crystal structure and function of a DARPin neutralizing inhibitor of lactococcal phage TP901-1: comparison of DARPin and camelid VHH binding mode.
  J Biol Chem, 284, 30718-30726.
PDB code: 3hg0
19719513 E.Scaltriti, M.Tegoni, C.Rivetti, H.Launay, J.Y.Masson, A.H.Magadan, D.Tremblay, S.Moineau, R.Ramoni, J.Lichière, V.Campanacci, C.Cambillau, and M.Ortiz-Lombardía (2009).
Structure and function of phage p2 ORF34(p2), a new type of single-stranded DNA binding protein.
  Mol Microbiol, 73, 1156-1170.
PDB codes: 2wkc 2wkd
19542338 G.M.Rousseau, and S.Moineau (2009).
Evolution of Lactococcus lactis phages within a cheese factory.
  Appl Environ Microbiol, 75, 5336-5344.  
19529959 J.Wesolowski, V.Alzogaray, J.Reyelt, M.Unger, K.Juarez, M.Urrutia, A.Cauerhff, W.Danquah, B.Rissiek, F.Scheuplein, N.Schwarz, S.Adriouch, O.Boyer, M.Seman, A.Licea, D.V.Serreze, F.A.Goldbaum, F.Haag, and F.Koch-Nolte (2009).
Single domain antibodies: promising experimental and therapeutic tools in infection and immunity.
  Med Microbiol Immunol, 198, 157-174.  
  19241371 K.Conrath, A.S.Pereira, C.E.Martins, C.G.Timóteo, P.Tavares, S.Spinelli, J.Kinne, C.Flaudrops, C.Cambillau, S.Muyldermans, I.Moura, J.J.Moura, M.Tegoni, and A.Desmyter (2009).
Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase.
  Protein Sci, 18, 619-628.  
19047351 M.Siponen, G.Sciara, M.Villion, S.Spinelli, J.Lichière, C.Cambillau, S.Moineau, and V.Campanacci (2009).
Crystal structure of ORF12 from Lactococcus lactis phage p2 identifies a tape measure protein chaperone.
  J Bacteriol, 191, 728-734.
PDB code: 3d8l
19286807 M.Siponen, S.Spinelli, S.Blangy, S.Moineau, C.Cambillau, and V.Campanacci (2009).
Crystal structure of a chimeric receptor binding protein constructed from two lactococcal phages.
  J Bacteriol, 191, 3220-3225.
PDB codes: 3d8m 3da0
19477632 S.Koide (2009).
Engineering of recombinant crystallization chaperones.
  Curr Opin Struct Biol, 19, 449-457.  
18045876 G.Sciara, S.Blangy, M.Siponen, S.Mc Grath, D.van Sinderen, M.Tegoni, C.Cambillau, and V.Campanacci (2008).
A topological model of the baseplate of lactococcal phage tuc2009.
  J Biol Chem, 283, 2716-2723.  
18374942 K.H.Choi, J.McPartland, I.Kaganman, V.D.Bowman, L.B.Rothman-Denes, and M.G.Rossmann (2008).
Insight into DNA and protein transport in double-stranded DNA viruses: the structure of bacteriophage N4.
  J Mol Biol, 378, 726-736.  
18539805 S.J.Labrie, J.Josephsen, H.Neve, F.K.Vogensen, and S.Moineau (2008).
Morphology, genome sequence, and structural proteome of type phage P335 from Lactococcus lactis.
  Appl Environ Microbiol, 74, 4636-4644.  
17875214 A.Hultberg, D.M.Tremblay, H.de Haard, T.Verrips, S.Moineau, L.Hammarström, and H.Marcotte (2007).
Lactobacillli expressing llama VHH fragments neutralise Lactococcus phages.
  BMC Biotechnol, 7, 58.  
17956421 S.Ostergaard Breum, H.Neve, K.J.Heller, and F.K.Vogensen (2007).
Temperate phages TP901-1 and phiLC3, belonging to the P335 species, apparently use different pathways for DNA injection in Lactococcus lactis subsp. cremoris 3107.
  FEMS Microbiol Lett, 276, 156-164.  
16547026 D.M.Tremblay, M.Tegoni, S.Spinelli, V.Campanacci, S.Blangy, C.Huyghe, A.Desmyter, S.Labrie, S.Moineau, and C.Cambillau (2006).
Receptor-binding protein of Lactococcus lactis phages: identification and characterization of the saccharide receptor-binding site.
  J Bacteriol, 188, 2400-2410.
PDB code: 1zru
16907729 J.Mahony, H.Deveau, S.Mc Grath, M.Ventura, C.Canchaya, S.Moineau, G.F.Fitzgerald, and D.van Sinderen (2006).
Sequence and comparative genomic analysis of lactococcal bacteriophages jj50, 712 and P008: evolutionary insights into the 936 phage species.
  FEMS Microbiol Lett, 261, 253-261.  
16940545 S.Ricagno, V.Campanacci, S.Blangy, S.Spinelli, D.Tremblay, S.Moineau, M.Tegoni, and C.Cambillau (2006).
Crystal structure of the receptor-binding protein head domain from Lactococcus lactis phage bIL170.
  J Virol, 80, 9331-9335.
PDB code: 2fsd
16549427 S.Spinelli, V.Campanacci, S.Blangy, S.Moineau, M.Tegoni, and C.Cambillau (2006).
Modular structure of the receptor binding proteins of Lactococcus lactis phages. The RBP structure of the temperate phage TP901-1.
  J Biol Chem, 281, 14256-14262.
PDB code: 2f0c
17053784 Y.Xiang, M.C.Morais, A.J.Battisti, S.Grimes, P.J.Jardine, D.L.Anderson, and M.G.Rossmann (2006).
Structural changes of bacteriophage phi29 upon DNA packaging and release.
  EMBO J, 25, 5229-5239.  
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.