PDBsum entry 2vmh

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Sugar-binding protein PDB id
Protein chain
147 a.a. *
Waters ×162
* Residue conservation analysis
PDB id:
Name: Sugar-binding protein
Title: The structure of cbm51 from clostridium perfringens gh95
Structure: Fibronectin type iii domain protein. Chain: a. Fragment: carbohydrate-binding module, residues 900-1050. Synonym: gh95cbm51. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 1502. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 511693.
1.50Å     R-factor:   0.150     R-free:   0.184
Authors: K.Gregg,R.Finn,D.W.Abbott,A.B.Boraston
Key ref:
K.J.Gregg et al. (2008). Divergent modes of glycan recognition by a new family of carbohydrate-binding modules. J Biol Chem, 283, 12604-12613. PubMed id: 18292090 DOI: 10.1074/jbc.M709865200
25-Jan-08     Release date:   19-Feb-08    
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Protein chain
Pfam   ArchSchema ?
Q0TP83  (Q0TP83_CLOP1) -  Fibronectin type III domain protein
1479 a.a.
147 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M709865200 J Biol Chem 283:12604-12613 (2008)
PubMed id: 18292090  
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
K.J.Gregg, R.Finn, D.W.Abbott, A.B.Boraston.
The genomes of myonecrotic Clostridium perfringens isolates contain genes encoding a large and fascinating array of highly modular glycoside hydrolase enzymes. Although the catalytic activities of many of these enzymes are somewhat predictable based on their amino acid sequences, the functions of their abundant ancillary modules are not and remain poorly studied. Here, we present the structural and functional analysis of a new family of ancillary carbohydrate-binding modules (CBMs), CBM51, which was previously annotated in data bases as the novel putative CBM domain. The high resolution crystal structures of two CBM51 members, GH95CBM51 and GH98CBM51, from a putative family 95 alpha-fucosidase and from a family 98 blood group A/B antigen-specific endo-beta-galactosidase, respectively, showed them to have highly similar beta-sandwich folds. However, GH95CBM51 was shown by glycan microarray screening, isothermal titration calorimetry, and x-ray crystallography to bind galactose residues, whereas the same analyses of GH98CBM51 revealed specificity for the blood group A/B antigens through non-conserved interactions. Overall, this work identifies a new family of CBMs with many members having apparent specificity for eukaryotic glycans, in keeping with the glycan-rich environment C. perfringens would experience in its host. However, a wider bioinformatic analysis of this CBM family also indicated a large number of members in non-pathogenic environmental bacteria, suggesting a role in the recognition of environmental glycans.
  Selected figure(s)  
Figure 3.
FIGURE 3. Fold and calcium binding of CBM51. Shown are color-ramped schematic representations of GH95CBM51 with methyl-β-D-galactose (A) and GH98CBM51 with the B antigen trisaccharide (B), both with bound calcium atoms shown as pink spheres and ligands in stick representation. C shows a schematic representation of CBM6-1 from Clostridium stercorarium (Protein Data Bank code 1uy4) (34), with its bound calcium atom shown as a pink sphere and its bound xylotetraose ligand shown in stick representation. This structure is a representative β-sandwich CBM showing the common calcium-binding site.
Figure 5.
FIGURE 5. Comparison of GH95CBM51, GH98CBM51, and other CBM51 members. A, overlay of the GH95CBM51 (yellow) and GH98CBM51 (magenta) carbohydrate-binding sites. Relevant side chains involved in binding and ligands are shown in stick representation, and the metal atoms are shown as spheres. B, phylogenetic analysis of CBM51. The inset shows the complete analysis and indicates the subfamilies. Subfamilies CBM51a and CBM51b (circled in the inset) are expanded with detailed entries. The green star denotes the GH98CBM51 entry, and the blue star denotes the GH95CBM51 entry. C, alignment of subfamilies CBM51a (indicated by the green vertical line) and CBM51b (indicated by the blue vertical line). The entry numbering corresponds to that in B. GH98CBM51 and GH95CBM51 are indicated by stars as in B. The secondary structures for GH98CBM51 and GH95CBM51 are shown above and below the alignment, respectively. Yellow arrows denote β-strands, and the red cylinder represents an -helix. Residues involved in ligand binding by GH98CBM51 and GH95CBM51 are indicated above and below the alignment, respectively, by arrowheads.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 12604-12613) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
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.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
19422833 E.Ficko-Blean, and A.B.Boraston (2009).
N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH.
  J Mol Biol, 390, 208-220.
PDB codes: 2w1q 2w1s 2w1u 2wdb
19426740 E.M.Grahn, H.C.Winter, H.Tateno, I.J.Goldstein, and U.Krengel (2009).
Structural characterization of a lectin from the mushroom Marasmius oreades in complex with the blood group B trisaccharide and calcium.
  J Mol Biol, 390, 457-466.
PDB code: 3ef2
19285508 M.A.Higgins, D.W.Abbott, M.J.Boulanger, and A.B.Boraston (2009).
Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae.
  J Mol Biol, 388, 299-309.
PDB code: 2w7y
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
19528664 M.E.Taylor, and K.Drickamer (2009).
Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands.
  Glycobiology, 19, 1155-1162.  
19171973 R.P.Joosten, T.Womack, G.Vriend, and G.Bricogne (2009).
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.
  Acta Crystallogr D Biol Crystallogr, 65, 176-185.  
18691891 D.C.Briggs, and A.J.Day (2008).
A bug in CUB's clothing: similarity between clostridial CBMs and complement CUBs.
  Trends Microbiol, 16, 407-408.  
18716000 J.J.Adams, K.Gregg, E.A.Bayer, A.B.Boraston, and S.P.Smith (2008).
Structural basis of Clostridium perfringens toxin complex formation.
  Proc Natl Acad Sci U S A, 105, 12194-12199.
PDB codes: 2ozn 2vo8
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.