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PDBsum entry 2wmf

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protein links
Hydrolase PDB id
2wmf
Jmol
Contents
Protein chain
555 a.a. *
Waters ×600
* Residue conservation analysis
PDB id:
2wmf
Name: Hydrolase
Title: Crystal structure of the catalytic module of a family 98 glycoside hydrolase from streptococcus pneumoniae tigr4 ( sp4gh98) in its native form.
Structure: Fucolectin-related protein. Chain: a. Fragment: catalytic module, residues 31-589. Synonym: glycoside hydrolase. Engineered: yes
Source: Streptococcus pneumoniae. Organism_taxid: 170187. Strain: tigr4. Atcc: baa-334. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.50Å     R-factor:   0.125     R-free:   0.159
Authors: M.A.Higgins,G.E.Whitworth,N.El Warry,M.Randriantsoa, E.Samain,R.D.Burke,D.J.Vocadlo,A.B.Boraston
Key ref:
M.A.Higgins et al. (2009). Differential recognition and hydrolysis of host carbohydrate antigens by Streptococcus pneumoniae family 98 glycoside hydrolases. J Biol Chem, 284, 26161-26173. PubMed id: 19608744 DOI: 10.1074/jbc.M109.024067
Date:
30-Jun-09     Release date:   14-Jul-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q97N96  (Q97N96_STRPN) -  Fucolectin-related protein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1038 a.a.
555 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
DOI no: 10.1074/jbc.M109.024067 J Biol Chem 284:26161-26173 (2009)
PubMed id: 19608744  
 
 
Differential recognition and hydrolysis of host carbohydrate antigens by Streptococcus pneumoniae family 98 glycoside hydrolases.
M.A.Higgins, G.E.Whitworth, N.El Warry, M.Randriantsoa, E.Samain, R.D.Burke, D.J.Vocadlo, A.B.Boraston.
 
  ABSTRACT  
 
The presence of a fucose utilization operon in the Streptococcus pneumoniae genome and its established importance in virulence indicates a reliance of this bacterium on the harvesting of host fucose-containing glycans. The identities of these glycans, however, and how they are harvested is presently unknown. The biochemical and high resolution x-ray crystallographic analysis of two family 98 glycoside hydrolases (GH98s) from distinctive forms of the fucose utilization operon that originate from different S. pneumoniae strains reveal that one enzyme, the predominant type among pneumococcal isolates, has a unique endo-beta-galactosidase activity on the LewisY antigen. Altered active site topography in the other species of GH98 enzyme tune its endo-beta-galactosidase activity to the blood group A and B antigens. Despite their different specificities, these enzymes, and by extension all family 98 glycoside hydrolases, use an inverting catalytic mechanism. Many bacterial and viral pathogens exploit host carbohydrate antigens for adherence as a precursor to colonization or infection. However, this is the first evidence of bacterial endoglycosidase enzymes that are known to play a role in virulence and are specific for distinct host carbohydrate antigens. The strain-specific distribution of two distinct types of GH98 enzymes further suggests that S. pneumoniae strains may specialize to exploit host-specific antigens that vary from host to host, a factor that may feature in whether a strain is capable of colonizing a host or establishing an invasive infection.
 
  Selected figure(s)  
 
Figure 3.
The structural features of S. pneumoniae family 98 enzymes.A, divergent stereo schematic representation of the structure of Sp4GH98. The N-terminal (α/β)[8] barrel housing the catalytic residues in shown in green, the C-terminal β-sandwich domain in purple, and the smaller intervening domain in yellow. Shown are solvent-accessible surface representations (gray) of the active site of Sp4GH98 containing the H disaccharide (shown in a stick representation) (B) and Sp3GH98 containing the A trisaccharide (shown in a stick representation) (C). Green, galactose; blue, fucose; magenta, N-acetylgalactosamine. The yellow mesh shows the maximum likelihood (27)/σ[a]-weighted (29) F[o] − F[c] maps for the carbohydrates (contoured at 3σ; 0.24 electrons/Å^3 for Sp4GH98 and 0.20 electrons/Å^3 for Sp3GH98). Subsites of the active site are labeled in white. D, schematic of the interactions in the −1 and −2 subsites of Sp4GH98 and Sp3GH98. Residues in black are conserved in both enzymes and labeled in black (Sp4GH98) or gray (Sp3GH98). Red residues are present only in Sp4GH98. E, schematic of the −2′ subsite of Sp3GH98. Black residues are shown for interactions that are conserved for the galactose of the B-antigen and the N-acetylgalactosamine of the A antigen. The red residue represents an interaction that is unique to the A antigen. F, divergent stereo representation of a structural overlay of the active sites of Sp4GH98 (blue) and Sp3GH98 (orange). The A trisaccharide product in the Sp3GH98 active site is shown in sticks and colored as in C. The loop protruding from the β-sandwich domain is shown in a schematic diagram representation. Trp^512 of Sp4GH98 that blocks the −2′ subsite in this protein is shown in a stick representation.
Figure 4.
Aglycon recognition in GH98 enzymes. Solvent-accessible surface representation (gray) of the active site of Sp4GH98E158A containing the Lewis^Y tetrasaccharide substrate (shown in a stick representation) (A) and Sp3GH98E558A containing the A-Lewis^Y pentasaccharide (shown in a stick representation) (B). Green, galactose; blue, fucose; cyan, N-acetylglucosamine; magenta, N-acetylgalactosamine. The yellow mesh shows the maximum likelihood/σ[a]-weighted F[o] − F[c] maps for the carbohydrates contoured at 2.5σ (0.16 electrons/Å^3) for Sp4GH98E158A and 3σ (0.22 electrons/Å^3) for Sp3GH98E558A. Subsites of the active site are labeled in white. C, representative overlay of the GH98 active site. All GH98 structures were overlaid. Because of the virtually identical positioning of the active site structures, the Sp3GH98 A trisaccharide complex was chosen as a reference point to display key features. The backbone of the Sp3GH98 A trisaccharide product complex is shown in a schematic diagram with relevant active site residues shown in a stick representation. The A trisaccharide sugar is shown as yellow sticks. The A-Lewis^Y pentasaccharide from the Sp3GH98E558A substrate complex is shown as green sticks. Residues in Sp3GH98 are labeled in gray, and analogous residues in Sp4GH98, which were identically positioned, are labeled in black. Sugar residues in the +1 and −1 subsites of Sp4GH98 were also positioned virtually identically to those of the Sp3GH98 complexes. Relevant interresidue hydrogen bonds and protein-substrate distances are shown. The putative catalytic acid is colored pink and putative catalytic bases are colored blue. D, schematic of the interactions in the +1 and +1′ subsites. Interactions conserved between Sp4GH98 and Sp3GH98 are shown with green amino acids. Black amino acids are those only in Sp4GH98, and red amino acids are those only in Sp3GH98.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 26161-26173) copyright 2009.  
  Figures were selected by an automated process.