PDBsum entry 2v5d

Go to PDB code: 
protein metals links
Hydrolase PDB id
Protein chain
722 a.a. *
_CA ×3
Waters ×27
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Structure of a family 84 glycoside hydrolase and a family 32 carbohydrate-binding module in tandem from clostridium perfringens.
Structure: O-glcnacase nagj. Chain: a. Fragment: residues 31-767. Synonym: beta-hexosaminidase, hexosaminidase b, gh84, n-acetyl-beta-glucosaminidase, beta-n-acetylhexosaminidase, family 84 glycoside hydrolase, family 32 carbohydrate binding module. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 1502. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 469008.
3.30Å     R-factor:   0.324     R-free:   0.369
Authors: E.Ficko-Blean,K.J.Gregg,J.J.Adams,J.H.Hehemann,S.J.Smith, M.Czjzek,A.B.Boraston
Key ref:
E.Ficko-Blean et al. (2009). Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens. J Biol Chem, 284, 9876-9884. PubMed id: 19193644 DOI: 10.1074/jbc.M808954200
02-Oct-08     Release date:   27-Jan-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q0TR53  (OGA_CLOP1) -  O-GlcNAcase NagJ
1001 a.a.
722 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.  - Protein O-GlcNAcase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
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
+ H(2)O
= [protein]- L-serine
+ N-acetyl-D-glucosamine
+ H(2)O
= [protein]-L-threonine
+ N-acetyl-D-glucosamine
   Enzyme class 2: E.C.  - Beta-N-acetylhexosaminidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   1 term 


DOI no: 10.1074/jbc.M808954200 J Biol Chem 284:9876-9884 (2009)
PubMed id: 19193644  
Portrait of an enzyme, a complete structural analysis of a multimodular {beta}-N-acetylglucosaminidase from Clostridium perfringens.
E.Ficko-Blean, K.J.Gregg, J.J.Adams, J.H.Hehemann, M.Czjzek, S.P.Smith, A.B.Boraston.
Common features of the extracellular carbohydrate-active virulence factors involved in host-pathogen interactions are their large sizes and modular complexities. This has made them recalcitrant to structural analysis, and therefore our understanding of the significance of modularity in these important proteins is lagging. Clostridium perfringens is a prevalent human pathogen that harbors a wide array of large, extracellular carbohydrate-active enzymes and is an excellent and relevant model system to approach this problem. Here we describe the complete structure of C. perfringens GH84C (NagJ), a 1001-amino acid multimodular homolog of the C. perfringens micro-toxin, which was determined using a combination of small angle x-ray scattering and x-ray crystallography. The resulting structure reveals unprecedented insight into how catalysis, carbohydrate-specific adherence, and the formation of molecular complexes with other enzymes via an ultra-tight protein-protein interaction are spatially coordinated in an enzyme involved in a host-pathogen interaction.
  Selected figure(s)  
Figure 2.
Structures of GH84C catalytic module and GH84C-CBM32 as determined using x-ray crystallography and SAXS. A and B show the crystal structures of GH84C catalytic module and GH84C-CBM32, respectively, in a ribbon representation. The arrow in B shows the C terminus of the CBM. C shows the GASBOR-generated SAXS envelope of GH84C-CBM32, whereas D shows the modules of GH84C-CBM32 manually fit into the SAXS envelope. E shows the model in D without the SAXS form. F shows the unmodified x-ray crystal structure, shown in B, fit into the SAXS-generated envelope. All of the structures are shown from identical orientations. The N-terminal domain is pictured in light blue, the catalytic TIM barrel is in orange, the helical bundle is in pale green, and the CBM in red.
Figure 4.
Structural features of the Coh-FN3 modular pair. A shows a ribbon representation of the 1.8-Å crystal structure of Coh-FN3. The Coh module is depicted in blue, and FN3 is shown in black. B shows the surface representation of Coh-FN3 colored according to electrostatic potential (red is negative, and blue is positive). The basic patch of FN3 is circled and expanded to show a patch of basic residues.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 9876-9884) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20640461 H.C.Dorfmueller, V.S.Borodkin, D.E.Blair, S.Pathak, I.Navratilova, and D.M.van Aalten (2011).
Substrate and product analogues as human O-GlcNAc transferase inhibitors.
  Amino Acids, 40, 781-792.
PDB codes: 2xgm 2xgo 2xgs
21483708 J.Marquay Markiewicz, S.Syan, C.C.Hon, C.Weber, D.Faust, and N.Guillen (2011).
A proteomic and cellular analysis of uropods in the pathogen Entamoeba histolytica.
  PLoS Negl Trop Dis, 5, e1002.  
20954171 M.Voronov-Goldman, R.Lamed, I.Noach, I.Borovok, M.Kwiat, S.Rosenheck, L.J.Shimon, E.A.Bayer, and F.Frolow (2011).
Noncellulosomal cohesin from the hyperthermophilic archaeon Archaeoglobus fulgidus.
  Proteins, 79, 50-60.
PDB code: 2xdh
20026047 H.C.Dorfmueller, and D.M.van Aalten (2010).
Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds.
  FEBS Lett, 584, 694-700.
PDB code: 2x0y
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.