PDBsum entry 4j5t

Hydrolase

PDB id: 4j5t

Contents

Protein chain

788 a.a.

Ligands

NAG ×4

Waters ×285

PDB id:

4j5t

Name:

Hydrolase

Title:

Crystal structure of processing alpha-glucosidase i

Structure:

Mannosyl-oligosaccharide glucosidase. Chain: a. Fragment: unp residues 31-833. Synonym: processing a-glucosidase i, glucosidase i. Engineered: yes

Source:

Saccharomyces cerevisiae. Yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Gene: cwh41, gls1, ygl027c. Expressed in: komagataella pastoris. Expression_system_taxid: 4922.

Resolution:

2.04Å R-factor: 0.226 R-free: 0.235

Authors:

M.K.Barker,D.R.Rose

Key ref:

M.K.Barker and D.R.Rose (2013). Specificity of Processing α-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies. J Biol Chem, 288, 13563-13574. PubMed id: 23536181 DOI: 10.1074/jbc.M113.460436

Date:

09-Feb-13 Release date: 03-Apr-13

Protein chain

P53008  (CWH41_YEAST) -  Mannosyl-oligosaccharide glucosidase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 833 a.a.

Struc: 788 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.106 - mannosyl-oligosaccharide glucosidase.
• Reaction: N₄-(alpha-D-Glc-(1->2)-alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D- Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)- alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man- (1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] + H2O = N₄-(alpha-D-Glc-(1->3)-alpha-D-Glc- (1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D- Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]- alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D- GlcNAc)-L-asparaginyl-[protein] + beta-D-glucose

N(4)-(alpha-D-Glc-(1->2)-alpha-D-Glc-(1->3)-alpha-D-Glc-(1->3)-alpha-D- Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)- alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man- (1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] + H2O = N(4)-(alpha-D-Glc-(1->3)-alpha-D-Glc- (1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D- Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]- alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D- GlcNAc)-L-asparaginyl-[protein] (Bound ligand (Het Group name = NAG) matches with 62.50% similarity) + beta-D-glucose

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M113.460436

J Biol Chem 288:13563-13574 (2013)

PubMed id: 23536181

Specificity of Processing α-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies.

M.K.Barker, D.R.Rose.

ABSTRACT

Processing α-glucosidase I (GluI) is a key member of the eukaryotic N-glycosylation processing pathway, selectively catalyzing the first glycoprotein trimming step in the endoplasmic reticulum. Inhibition of GluI activity impacts the infectivity of enveloped viruses; however, despite interest in this protein from a structural, enzymatic, and therapeutic standpoint, little is known about its structure and enzymatic mechanism in catalysis of the unique glycan substrate Glc3Man9GlcNAc2. The first structural model of eukaryotic GluI is here presented at 2-Å resolution. Two catalytic residues are proposed, mutations of which result in catalytically inactive, properly folded protein. Using Autodocking methods with the known substrate and inhibitors as ligands, including a novel inhibitor characterized in this work, the active site of GluI was mapped. From these results, a model of substrate binding has been formulated, which is most likely conserved in mammalian GluI.