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Hydrolase PDB id
3fhq
Jmol
Contents
Protein chains
601 a.a. *
Ligands
BMA-MAN-MAN-NGT ×4
Waters ×837
* Residue conservation analysis
PDB id:
3fhq
Name: Hydrolase
Title: Structure of endo-beta-n-acetylglucosaminidase a
Structure: Endo-beta-n-acetylglucosaminidase. Chain: a, b, d, f. Fragment: unp residues 25-645. Synonym: endo-beta-n-acetylglucosaminidase a. Engineered: yes. Mutation: yes
Source: Arthrobacter protophormiae. Organism_taxid: 37930. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.45Å     R-factor:   0.223     R-free:   0.264
Authors: Y.Jie,L.Li,N.Shaw,Y.Li,J.Song,W.Zhang,C.Xia,R.Zhang, A.Joachimiak,H.-C.Zhang,L.-X.Wang,P.Wang,Z.-J.Liu
Key ref: J.Yin et al. (2009). Structural basis and catalytic mechanism for the dual functional endo-beta-N-acetylglucosaminidase A. Plos One, 4, e4658. PubMed id: 19252736 DOI: 10.1371/journal.pone.0004658
Date:
10-Dec-08     Release date:   05-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9ZB22  (Q9ZB22_9MICC) -  Endo-beta-N-acetylglucosaminidase
Seq:
Struc: 		 
Seq:
Struc: 		645 a.a.
601 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.96  - Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of the di-N-acetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -[Man(GlcNAc)2]Asn- structure. One N-acetyl-D-glucosamine residue remains attached to the protein; the rest of the oligosaccharide is released intact.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
DOI no: 10.1371/journal.pone.0004658 Plos One 4:e4658 (2009)
PubMed id: 19252736  
 
 
Structural basis and catalytic mechanism for the dual functional endo-beta-N-acetylglucosaminidase A.
J.Yin, L.Li, N.Shaw, Y.Li, J.K.Song, W.Zhang, C.Xia, R.Zhang, A.Joachimiak, H.C.Zhang, L.X.Wang, Z.J.Liu, P.Wang.
 
  ABSTRACT  
 
Endo-beta-N-acetylglucosaminidases (ENGases) are dual specificity enzymes with an ability to catalyze hydrolysis and transglycosylation reactions. Recently, these enzymes have become the focus of intense research because of their potential for synthesis of glycopeptides. We have determined the 3D structures of an ENGase from Arthrobacter protophormiae (Endo-A) in 3 forms, one in native form, one in complex with Man(3)GlcNAc-thiazoline and another in complex with GlcNAc-Asn. The carbohydrate moiety sits above the TIM-barrel in a cleft region surrounded by aromatic residues. The conserved essential catalytic residues - E173, N171 and Y205 are within hydrogen bonding distance of the substrate. W216 and W244 regulate access to the active site during transglycosylation by serving as "gate-keepers". Interestingly, Y299F mutation resulted in a 3 fold increase in the transglycosylation activity. The structure provides insights into the catalytic mechanism of GH85 family of glycoside hydrolases at molecular level and could assist rational engineering of ENGases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21104698 C.R.Santos, C.C.Tonoli, D.M.Trindade, C.Betzel, H.Takata, T.Kuriki, T.Kanai, T.Imanaka, R.K.Arni, and M.T.Murakami (2011).
Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  Proteins, 79, 547-557.
PDB codes: 3n8t 3n92 3n98
20673219 J.Li, C.L.Huang, L.W.Zhang, L.Lin, Z.H.Li, F.W.Zhang, and P.Wang (2010).
Isoforms of human O-GlcNAcase show distinct catalytic efficiencies.
  Biochemistry (Mosc), 75, 938-943.  
19880511 M.Umekawa, C.Li, T.Higashiyama, W.Huang, H.Ashida, K.Yamamoto, and L.X.Wang (2010).
Efficient glycosynthase mutant derived from Mucor hiemalis endo-beta-N-acetylglucosaminidase capable of transferring oligosaccharide from both sugar oxazoline and natural N-glycan.
  J Biol Chem, 285, 511-521.  
20449490 T.B.Parsons, M.K.Patel, A.B.Boraston, D.J.Vocadlo, and A.J.Fairbanks (2010).
Streptococcus pneumoniae endohexosaminidase D; feasibility of using N-glycan oxazoline donors for synthetic glycosylation of a GlcNAc-asparagine acceptor.
  Org Biomol Chem, 8, 1861-1869.  
20486148 W.Huang, Q.Yang, M.Umekawa, K.Yamamoto, and L.X.Wang (2010).
Arthrobacter endo-beta-N-acetylglucosaminidase shows transglycosylation activity on complex-type N-glycan oxazolines: one-pot conversion of ribonuclease B to sialylated ribonuclease C.
  Chembiochem, 11, 1350-1355.  
19766528 L.X.Wang, and W.Huang (2009).
Enzymatic transglycosylation for glycoconjugate synthesis.
  Curr Opin Chem Biol, 13, 592-600.  
19754974 X.Shao, M.Jiang, Z.Yu, H.Cai, and L.Li (2009).
Surface display of heterologous proteins in Bacillus thuringiensis using a peptidoglycan hydrolase anchor.
  Microb Cell Fact, 8, 48.  
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.