PDBsum entry: 3fhq

Hydrolase

PDB-id: 3fhq

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PROCHECK

Protein chains

601 a.a. *

Ligands

BMA-MAN-MAN-NGT ×4

Waters ×837

* Residue conservation analysis

Tools

Clefts Calculation

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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.

UniProt:

Chains A, B, D, F: Q9ZB22 (Q9ZB22_9MICC)

Seq:

Struc:

Seq:

Struc:

Seq:

645 a.a.

Struc:

601 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme class:

E.C.3.2.1.96   [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.

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

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Surface

Key reference

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.