PDBsum entry 2vc9

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Hydrolase PDB id
Protein chain
884 a.a. *
GOL ×2
Waters ×391
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Family 89 glycoside hydrolase from clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin
Structure: Alpha-n-acetylglucosaminidase. Chain: a. Fragment: residues 26-916. Engineered: yes
Source: Clostridium perfringens. Organism_taxid: 1502. Atcc: 13124. Expressed in: escherichia coli. Expression_system_taxid: 469008.
2.36Å     R-factor:   0.205     R-free:   0.246
Authors: E.Ficko-Blean,K.A.Stubbs,O.Berg,D.J.Vocadlo,A.B.Boraston
Key ref:
E.Ficko-Blean et al. (2008). Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB. Proc Natl Acad Sci U S A, 105, 6560-6565. PubMed id: 18443291 DOI: 10.1073/pnas.0711491105
19-Sep-07     Release date:   18-Mar-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q0TST1  (Q0TST1_CLOP1) -  Alpha-N-acetylglucosaminidase family protein
2095 a.a.
884 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell adhesion   1 term 


DOI no: 10.1073/pnas.0711491105 Proc Natl Acad Sci U S A 105:6560-6565 (2008)
PubMed id: 18443291  
Structural and mechanistic insight into the basis of mucopolysaccharidosis IIIB.
E.Ficko-Blean, K.A.Stubbs, O.Nemirovsky, D.J.Vocadlo, A.B.Boraston.
Mucopolysaccharidosis III (MPS III) has four forms (A-D) that result from buildup of an improperly degraded glycosaminoglycan in lysosomes. MPS IIIB is attributable to the decreased activity of a lysosomal alpha-N-acetylglucosaminidase (NAGLU). Here, we describe the structure, catalytic mechanism, and inhibition of CpGH89 from Clostridium perfringens, a close bacterial homolog of NAGLU. The structure enables the generation of a homology model of NAGLU, an enzyme that has resisted structural studies despite having been studied for >20 years. This model reveals which mutations giving rise to MPS IIIB map to the active site and which map to regions distant from the active site. The identification of potent inhibitors of CpGH89 and the structures of these inhibitors in complex with the enzyme suggest small-molecule candidates for use as chemical chaperones. These studies therefore illuminate the genetic basis of MPS IIIB, provide a clear biochemical rationale for the necessary sequential action of heparan-degrading enzymes, and open the door to the design and optimization of chemical chaperones for treating MPS IIIB.
  Selected figure(s)  
Figure 2.
Structural location of naturally occurring mutations in NAGLU. (A) A cartoon representation of the homology model of NAGLU showing its overall fold. The coloring of the domains is as for CpGH89 in Fig. 1A. (B) A structural overlay of the active site of CpGH89 and NAGLU. The catalytic residues are labeled. (C) A view of the ribbon trace of the NAGLU model with the structural location of the known mutations that lead to MPS IIIB. Sites of mutations are shown as spheres. Blue coloring indicates active site residues, whereas red coloring indicates nonactive site residues.
Figure 3.
Inhibitor binding by CpGH89. (A and B) Isotherms of CpGH89 binding to PUGNAc (A) and 2AcDNJ (B) produced by ITC. (Upper) Raw heat measurements. (Lower) Integrated heats. The solid lines show the fit of a one site-binding model to the data. (A Inset) Dixon plot analysis of CpGH89 inhibition by PUGNAc. The intersection point on the graph corresponding to the K [i] (absolute value of the X value at the intersection) is indicated by an arrow. (C and D ) Active site representations are shown for PUGNAc (C ) and 2AcDNJ (D). The blue mesh shows the maximum likelihood (43)/σ[a] (49)-weighted electron density maps contoured at 0.23 e^−/Å^3 and 0.22 e^−/Å^3 for 2AcDNJ and PUGNAc, respectively. Key active site residues, including the putative catalytic residues Glu-483 and Glu-601, are shown in stick representation and colored gray. Ligands are shown in green stick representation. Putative hydrogen bonds between the protein and ligand identified by using the criteria of proper geometry and a distance cutoff of 3.2 Å are shown as dotted magenta lines. (E and F ) Schematics showing the interactions within the active site of CpGH89 with PUGNAc (E ) and 2AcDNJ (F ). A distance of 3.2 Å was used as the cutoff for significant hydrogen bonds. Water molecules are shown as shaded spheres. Protons on the amino acids are omitted for clarity.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20665773 A.Lammerts van Bueren, S.D.Popat, C.H.Lin, and G.J.Davies (2010).
Structural and thermodynamic analyses of α-L-fucosidase inhibitors.
  Chembiochem, 11, 1971-1974.
PDB codes: 2xib 2xii
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
20851343 M.S.Macauley, Y.He, T.M.Gloster, K.A.Stubbs, G.J.Davies, and D.J.Vocadlo (2010).
Inhibition of O-GlcNAcase using a potent and cell-permeable inhibitor does not induce insulin resistance in 3T3-L1 adipocytes.
  Chem Biol, 17, 937-948.
PDB code: 2xj7
20396401 T.M.Gloster, and D.J.Vocadlo (2010).
Mechanism, Structure, and Inhibition of O-GlcNAc Processing Enzymes.
  Curr Signal Transduct Ther, 5, 74-91.  
19273679 A.Asgarali, K.A.Stubbs, A.Oliver, D.J.Vocadlo, and B.L.Mark (2009).
Inactivation of the glycoside hydrolase NagZ attenuates antipseudomonal beta-lactam resistance in Pseudomonas aeruginosa.
  Antimicrob Agents Chemother, 53, 2274-2282.  
19181667 D.W.Abbott, M.S.Macauley, D.J.Vocadlo, and A.B.Boraston (2009).
Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases.
  J Biol Chem, 284, 11676-11689.
PDB codes: 2w91 2w92
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
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18706999 M.von Itzstein (2008).
Disease-associated carbohydrate-recognising proteins and structure-based inhibitor design.
  Curr Opin Struct Biol, 18, 558-566.  
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.