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PDBsum entry 2w7y

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protein ligands metals Protein-protein interface(s) links
Sugar-binding protein PDB id
2w7y
Jmol
Contents
Protein chains
389 a.a. *
Ligands
A2G-GAL-FUC ×2
Metals
IOD ×2
Waters ×410
* Residue conservation analysis
PDB id:
2w7y
Name: Sugar-binding protein
Title: Structure of a streptococcus pneumoniae solute-binding protein in complex with the blood group a-trisaccharide.
Structure: Probable sugar abc transporter, sugar-binding protein. Chain: a, b. Fragment: solute-binding protein, residues 24-430. Synonym: fcssbp. Engineered: yes
Source: Streptococcus pneumoniae. Organism_taxid: 406556. Strain: sp3-bs71. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.35Å     R-factor:   0.215     R-free:   0.263
Authors: M.A.Higgins,D.W.Abbott,M.J.Boulanger,A.B.Boraston
Key ref:
M.A.Higgins et al. (2009). Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae. J Mol Biol, 388, 299-309. PubMed id: 19285508 DOI: 10.1016/j.jmb.2009.03.012
Date:
06-Jan-09     Release date:   10-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
A5LBQ6  (A5LBQ6_STRPN) -  Probable sugar ABC transporter, sugar-binding protein
Seq:
Struc:
430 a.a.
389 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     transport   1 term 
  Biochemical function     transporter activity     1 term  

 

 
DOI no: 10.1016/j.jmb.2009.03.012 J Mol Biol 388:299-309 (2009)
PubMed id: 19285508  
 
 
Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae.
M.A.Higgins, D.W.Abbott, M.J.Boulanger, A.B.Boraston.
 
  ABSTRACT  
 
Streptococcus pneumoniae is a common bacterial pathogen that is well known for its ability to cause acute respiratory disease (pneumonia), ear infections, and other serious illnesses. This Gram-positive bacterium relies on its carbohydrate-metabolizing capabilities for full virulence in its host; however, the range of glycan targets that it can attack is presently not fully appreciated. S. pneumoniae is known to have a fucose utilization operon that in the TIGR4 strain plays a role in its virulence. Here we identify a second type of fucose utilization operon that is present in a subset of S. pneumoniae strains, including the serotype 3 strain SP3-BS71. This operon contains a transporter with a solute-binding protein, FcsSBP (fucose solute-binding protein), that interacts tightly (Ka approximately 1 x 10(6) M(-1)) and specifically with soluble A- and B-antigen trisaccharides but displays no selectivity between these two sugars. The structure of the FcsSBP in complex with the A-trisaccharide antigen, determined to 2.35 A, reveals its mode of binding to the reducing end of this sugar, thus highlighting this protein's requirement for soluble blood group antigen ligands. Overall, this report exposes a heretofore unknown capability of certain S. pneumoniae strains to transport and potentially metabolize the histo-blood group antigen carbohydrates of its host.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. X-ray crystal structure of the FcsSBP from S. pneumoniae SP3-BS71. (a) The divergent stereo diagram of the FcsSBP structure shows the bilobed structure of the protein and the general location of the ligand-binding site. The blood group A-trisaccharide ligand is shown in green stick representation. (b) The high quality of the electron density of the bound A-trisaccharide ligand is shown in the divergent stereo maximum-likelihood/σ[a]-weighted F[obs] − F[calc] maps^[28]^ and ^[29] (contoured at 3σ = 0.21 e^−/Å^2) produced by refinement of the FcsSBP structure with the A-trisaccharide coordinates omitted. The electron density is shown as blue mesh, while the ligand is shown in stick representation (green, fucose; pink, galactose; and blue/cyan, GalNAc). (c) The binding site of the FcsSBP is a deep pocket formed upon the convergence of the N- and C-terminal domains. The reducing end of the sugar (indicated with a yellow arrow) pointing into the binding site. The sugar is color coded as in (b), with the protein shown as a solvent-accessible surface colored by electrostatic potential (red, negative; blue, positive). (d) The aromatic “cradle” of the active site comprises three side chains, which are shown in grey stick representation and labelled. The ligand is shown as in (c). (e) Hydrogen-bonding schematic of the binding site. The contributions of amino acids from the N- and C-terminal domains are indicated with an N and a C, respectively.
Figure 4.
Fig. 4. Alignment of FcsSBP with its most closely related proteins in the database. Streptococcus denotes FcsSBP from S. pneumoniae SP3-BS71, Ruminococcus denotes RUMGNA_03829 from R. gnavus (ATCC 29149), and Clostridium denotes CLOSCI_02090 from C. scindens (ATCC 35704). The secondary structure of FcsSBP is indicated above the sequence. Residues in FcsSBP that are involved in hydrogen bonding with substrate are indicated above the alignment by green shapes (green triangle, hydrogen bonding only; green circle, apolar and hydrogen-bonding interaction). Aromatic residues involved in apolar interactions are indicated by circles (yellow circle, apolar interaction only; green circle, apolar and hydrogen-bonding interaction.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 299-309) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21256510 A.L.Morrow, J.Meinzen-Derr, P.Huang, K.R.Schibler, T.Cahill, M.Keddache, S.G.Kallapur, D.S.Newburg, M.Tabangin, B.B.Warner, and X.Jiang (2011).
Fucosyltransferase 2 non-secretor and low secretor status predicts severe outcomes in premature infants.
  J Pediatr, 158, 745-751.  
21423604 D.Garrido, J.H.Kim, J.B.German, H.E.Raybould, and D.A.Mills (2011).
Oligosaccharide binding proteins from Bifidobacterium longum subsp. infantis reveal a preference for host glycans.
  PLoS One, 6, e17315.  
20976527 F.Strino, J.H.Lii, C.A.Koppisetty, P.G.Nyholm, and H.J.Gabius (2010).
Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity.
  J Comput Aided Mol Des, 24, 1009-1021.  
19663501 A.Eshghi, P.A.Cullen, L.Cowen, R.L.Zuerner, and C.E.Cameron (2009).
Global proteome analysis of Leptospira interrogans.
  J Proteome Res, 8, 4564-4578.  
19608744 M.A.Higgins, G.E.Whitworth, N.El Warry, M.Randriantsoa, E.Samain, R.D.Burke, D.J.Vocadlo, and A.B.Boraston (2009).
Differential recognition and hydrolysis of host carbohydrate antigens by Streptococcus pneumoniae family 98 glycoside hydrolases.
  J Biol Chem, 284, 26161-26173.
PDB codes: 2wmf 2wmg 2wmh 2wmi 2wmj 2wmk
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