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PDBsum entry 2bq9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2bq9
Jmol
Contents
Protein chains
601 a.a.
Ligands
GAL ×3
GOL ×3
Metals
_NA ×3
Waters ×1494
Superseded by: 2bzd 2bzd
PDB id:
2bq9
Name: Hydrolase
Title: Galactose recognition by the carbohydrate-binding module of a bacterial sialidase
Structure: Bacterial sialidase. Synonym: neuraminidase. Chain: a, b, c. Fragment: residues 47-647. Mutation: yes. Engineered: yes
Source: Expressed in: escherichia coli. Micromonospora viridifaciens. Atcc: 31146
Resolution:
2.00Å     R-factor:   0.186     R-free:   0.258
Authors: S.L.Newstead,G.L.Taylor
Key ref:
S.L.Newstead et al. (2005). Galactose recognition by the carbohydrate-binding module of a bacterial sialidase. Acta Crystallogr D Biol Crystallogr, 61, 1483-1491. PubMed id: 16239725 DOI: 10.1107/S0907444905026132
Date:
27-Apr-05     Release date:   29-Apr-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q02834  (NANH_MICVI) -  Sialidase
Seq:
Struc:
 
Seq:
Struc:
647 a.a.
601 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.18  - Exo-alpha-sialidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.

 

 
DOI no: 10.1107/S0907444905026132 Acta Crystallogr D Biol Crystallogr 61:1483-1491 (2005)
PubMed id: 16239725  
 
 
Galactose recognition by the carbohydrate-binding module of a bacterial sialidase.
S.L.Newstead, J.N.Watson, A.J.Bennet, G.Taylor.
 
  ABSTRACT  
 
Glycoside hydrolases often possess carbohydrate-binding modules (CBMs) in addition to their catalytic domains, which help target the enzymes to appropriate substrates and thereby increase their catalytic efficiency. Sialidases hydrolyse the release of sialic acid from a variety of glycoconjugates and play significant roles in the pathogenesis of a number of important diseases. The sialidase from Micromonospora viridifaciens has a CBM which recognizes galactose. The CBM is linked to the catalytic domain by an immunoglobulin-like domain, resulting in the galactose binding site sitting above the catalytic site, suggesting an interplay between the two sites. By studying nine crystallographically independent structures of the M. viridifaciens sialidase, the relative flexibility of the three domains was analysed. A detailed study is also presented of the recognition of galactose and lactose by the M. viridifaciens CBM. The striking structure of this sialidase suggests a role for the CBM in binding to galactose residues unmasked by the adjacent catalytic site.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 (a) and (b) Orthogonal views of the M. viridifaciens sialidase. The catalytic domain (47-403) is in light brown with Neu5Ac2en bound in the active site, the immunoglobulin-like domain (403-505) is in green and the CBM (505-647) is in cyan with lactose bound. The metal ion is shown as a magenta ball. The disulfide between 351-405 linking the first two domains is also shown. (c) Molecular surface coloured according to electrostatic potential; same view as in (a).
Figure 2.
Figure 2 The galactose-binding site of the CBM. (a) and (b) show 2F[obs] - F[calc] electron-density maps for the galactose and lactose, respectively, contoured at 0.6 e -3 (approximately 2 [142][sigma] ). (c) and (d) show stereoviews of the binding site with galactose and lactose bound, respectively. Hydrogen bonds are drawn in green and waters are shown as magenta spheres.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1483-1491) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21240549 T.Lieke, D.Gröbe, V.Blanchard, D.Grunow, R.Tauber, M.Zimmermann-Kordmann, T.Jacobs, and W.Reutter (2011).
Invasion of Trypanosoma cruzi into host cells is impaired by N-propionylmannosamine and other N-acylmannosamines.
  Glycoconj J, 28, 31-37.  
19908036 D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.
  Appl Microbiol Biotechnol, 85, 1241-1249.  
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
19594936 E.M.Quistgaard, and S.S.Thirup (2009).
Sequence and structural analysis of the Asp-box motif and Asp-box beta-propellers; a widespread propeller-type characteristic of the Vps10 domain family and several glycoside hydrolase families.
  BMC Struct Biol, 9, 46.  
19458903 J.Uhlendorff, T.Matrosovich, H.D.Klenk, and M.Matrosovich (2009).
Functional significance of the hemadsorption activity of influenza virus neuraminidase and its alteration in pandemic viruses.
  Arch Virol, 154, 945-957.  
19191477 N.Koropatkin, E.C.Martens, J.I.Gordon, and T.J.Smith (2009).
Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.
  Biochemistry, 48, 1532-1542.
PDB codes: 3ehm 3ehn
19930717 Y.M.Cheng, F.C.Hsieh, and M.Meng (2009).
Functional analysis of conserved aromatic amino acids in the discoidin domain of Paenibacillus beta-1,3-glucanase.
  Microb Cell Fact, 8, 62.  
18986251 J.D.Glasner, M.Marquez-Villavicencio, H.S.Kim, C.E.Jahn, B.Ma, B.S.Biehl, A.I.Rissman, B.Mole, X.Yi, C.H.Yang, J.L.Dangl, S.R.Grant, N.T.Perna, and A.O.Charkowski (2008).
Niche-specificity and the variable fraction of the Pectobacterium pan-genome.
  Mol Plant Microbe Interact, 21, 1549-1560.  
18218621 S.L.Newstead, J.A.Potter, J.C.Wilson, G.Xu, C.H.Chien, A.G.Watts, S.G.Withers, and G.L.Taylor (2008).
The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.
  J Biol Chem, 283, 9080-9088.
PDB codes: 2bf6 2vk5 2vk6 2vk7
17322533 S.Mouilleron, and B.Golinelli-Pimpaneau (2007).
Domain motions of glucosamine-6P synthase: comparison of the anisotropic displacements in the crystals and the catalytic hinge-bending rotation.
  Protein Sci, 16, 485-493.  
16990278 E.Ficko-Blean, and A.B.Boraston (2006).
The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.
  J Biol Chem, 281, 37748-37757.
PDB codes: 2j1a 2j1e 2j1f 2j7m
16565725 R.J.Dennis, E.J.Taylor, M.S.Macauley, K.A.Stubbs, J.P.Turkenburg, S.J.Hart, G.N.Black, D.J.Vocadlo, and G.J.Davies (2006).
Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity.
  Nat Struct Mol Biol, 13, 365-371.
PDB codes: 2chn 2cho
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.