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PDBsum entry 2j1e

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protein ligands metals links
Hydrolase PDB id
2j1e
Jmol
Contents
Protein chain
142 a.a. *
Ligands
NDG-GAL
Metals
_CA
Waters ×176
* Residue conservation analysis
PDB id:
2j1e
Name: Hydrolase
Title: High resolution crystal structure of cbm32 from a n-acetyl- beta-hexosaminidase in complex with lacnac
Structure: Hyaluronidase. Chain: a. Fragment: carbohydrate binding module, residues 625-767. Synonym: cbm32. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 195103. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.179     R-free:   0.252
Authors: E.Ficko-Blean,A.B.Boraston
Key ref:
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. PubMed id: 16990278 DOI: 10.1074/jbc.M606126200
Date:
10-Aug-06     Release date:   20-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8XL08  (OGA_CLOPE) -  O-GlcNAcase NagJ
Seq:
Struc:
 
Seq:
Struc:
1001 a.a.
142 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.169  - Protein O-GlcNAcase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. [Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine + H2O = [protein]- L-serine + N-acetyl-D-glucosamine
2. [Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine + H2O = [protein]-L-threonine + N-acetyl-D-glucosamine
[Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine
+ H(2)O
= [protein]- L-serine
+ N-acetyl-D-glucosamine
[Protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine
+ H(2)O
= [protein]-L-threonine
+ N-acetyl-D-glucosamine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell adhesion   1 term 

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M606126200 J Biol Chem 281:37748-37757 (2006)
PubMed id: 16990278  
 
 
The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor.
E.Ficko-Blean, A.B.Boraston.
 
  ABSTRACT  
 
Clostridium perfringens is a notable colonizer of the human gastrointestinal tract. This bacterium is quite remarkable for a human pathogen by the number of glycoside hydrolases found in its genome. The modularity of these enzymes is striking as is the frequent occurrence of modules having amino acid sequence identity with family 32 carbohydrate-binding modules (CBMs), often referred to as F5/8 domains. Here we report the properties of family 32 CBMs from a C. perfringens N-acetyl-beta-hexosaminidase. Macroarray, UV difference, and isothermal titration calorimetry binding studies indicate a preference for the disaccharide LacNAc (beta-d-galactosyl-1,4-beta-d-N-acetylglucosamine). The molecular details of the interaction of this CBM with galactose, LacNAc, and the type II blood group H-trisaccharide are revealed by x-ray crystallographic studies at resolutions of 1.49, 2.4, and 2.3 A, respectively.
 
  Selected figure(s)  
 
Figure 4.
FIGURE 4. Representative electron density and interaction of CpCBM32 with galactose (A), LacNAc (B), and the type II blood group H-trisaccharide (C). All maps are maximum-likelihood/ [A] (37)-weighted 2F[obs] - F[calc] electron density maps contoured at 1 (0.35, 0.30, and 0.29 electrons/Å^3 for galactose, LacNAc, and the H-trisaccharide, respectively). The disordered loop in the galactose complex is shown with a dashed line. Amino acid side chains involved in binding the sugars are shown in gray stick representation and labeled.
Figure 5.
FIGURE 5. Schematics showing the interactions of CpCBM32 with galactose (A), LacNAc (B), and the type II blood group H-trisaccharide (C). A distance of 3.2 Å was used as the cut-off for determination of significant hydrogen bonds. Water molecules are shown as shaded spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 37748-37757) copyright 2006.  
  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.  
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
21150123 S.Fushinobu (2010).
Unique sugar metabolic pathways of bifidobacteria.
  Biosci Biotechnol Biochem, 74, 2374-2384.  
19025568 A.Peer, S.P.Smith, E.A.Bayer, R.Lamed, and I.Borovok (2009).
Noncellulosomal cohesin- and dockerin-like modules in the three domains of life.
  FEMS Microbiol Lett, 291, 1.  
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
19193644 E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, M.Czjzek, S.P.Smith, and A.B.Boraston (2009).
Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.
  J Biol Chem, 284, 9876-9884.
PDB codes: 2v5c 2v5d 2w1n
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.  
18443291 E.Ficko-Blean, K.A.Stubbs, O.Nemirovsky, D.J.Vocadlo, and A.B.Boraston (2008).
Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.
  Proc Natl Acad Sci U S A, 105, 6560-6565.
PDB codes: 2vc9 2vca 2vcb 2vcc
18484336 F.J.Stevens (2008).
Possible evolutionary links between immunoglobulin light chains and other proteins involved in amyloidosis.
  Amyloid, 15, 96.  
18378588 H.Brüggemann, and G.Gottschalk (2008).
Comparative genomics of clostridia: link between the ecological niche and cell surface properties.
  Ann N Y Acad Sci, 1125, 73-81.  
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
18469123 J.Wada, T.Ando, M.Kiyohara, H.Ashida, M.Kitaoka, M.Yamaguchi, H.Kumagai, T.Katayama, and K.Yamamoto (2008).
Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure.
  Appl Environ Microbiol, 74, 3996-4004.  
18292090 K.J.Gregg, R.Finn, D.W.Abbott, and A.B.Boraston (2008).
Divergent modes of glycan recognition by a new family of carbohydrate-binding modules.
  J Biol Chem, 283, 12604-12613.
PDB codes: 2vmg 2vmh 2vmi 2vng 2vno 2vnr
18183385 M.Nakajima, T.Nihira, M.Nishimoto, and M.Kitaoka (2008).
Identification of galacto-N-biose phosphorylase from Clostridium perfringens ATCC13124.
  Appl Microbiol Biotechnol, 78, 465-471.  
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
18516288 R.M.Weiner, L.E.Taylor, B.Henrissat, L.Hauser, M.Land, P.M.Coutinho, C.Rancurel, E.H.Saunders, A.G.Longmire, H.Zhang, E.A.Bayer, H.J.Gilbert, F.Larimer, I.B.Zhulin, N.A.Ekborg, R.Lamed, P.M.Richardson, I.Borovok, and S.Hutcheson (2008).
Complete genome sequence of the complex carbohydrate-degrading marine bacterium, Saccharophagus degradans strain 2-40 T.
  PLoS Genet, 4, e1000087.  
18034207 J.Finsterer, and B.Hess (2007).
Neuromuscular and central nervous system manifestations of Clostridium perfringens infections.
  Infection, 35, 396-405.  
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.