PDBsum entry 5iee

Hydrolase

PDB id: 5iee

Contents

Protein chains

857 a.a.

88 a.a.

Ligands

NAG-NAG

PG4 ×3

P6G ×4

EDO ×6

FMT ×10

NOJ

Metals

_CA ×2

Waters ×950

PDB id:

5iee

Name:

Hydrolase

Title:

Murine endoplasmic reticulum alpha-glucosidase ii with 1- deoxynojirimycin

Structure:

Neutral alpha-glucosidase ab. Chain: a. Synonym: alpha-glucosidase 2,glucosidase ii subunit alpha. Engineered: yes. Other_details: this chain contains all of the residues from the mature q8bhn3 isoform 2 (i.E. No signal peptide and starts at residue 33) but has been trypsinised so that there are two gaps in the sequence between: 186-243 and 351-369 (inclusive). Glucosidase 2 subunit beta.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: ganab, g2an, kiaa0088. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek 293-f. Expression_system_organ: kidney. Expression_system_cell: endothelial.

Resolution:

1.92Å R-factor: 0.166 R-free: 0.196

Authors:

A.T.Caputo,P.Roversi,D.S.Alonzi,J.L.Kiappes,N.Zitzmann

Key ref:

A.T.Caputo et al. (2016). Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals. Proc Natl Acad Sci U S A, 113, E4630. PubMed id: 27462106 DOI: 10.1073/pnas.1604463113

Date:

25-Feb-16 Release date: 27-Jul-16

Protein chain

Q8BHN3  (GANAB_MOUSE) -  Neutral alpha-glucosidase AB from Mus musculus

Seq: 944 a.a.

Struc: 857 a.a.

Protein chain

O08795  (GLU2B_MOUSE) -  Glucosidase 2 subunit beta from Mus musculus

Seq: 521 a.a.

Struc: 88 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.3.2.1.207 - mannosyl-oligosaccharide alpha-1,3-glucosidase.
• Reaction:
  1. 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] + H2O = N₄-(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
  2. N₄-(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-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->6CC -!- This eukaryotic enzyme cleaves off sequentially the two alpha-1,3-

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] + H2O = N(4)-(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

N(4)-(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-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->6CC -!- This eukaryotic enzyme cleaves off sequentially the two alpha-1,3- (Bound ligand (Het Group name = NAG) matches with 62.50% similarity)

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

Key reference

DOI no: 10.1073/pnas.1604463113

Proc Natl Acad Sci U S A 113:E4630 (2016)

PubMed id: 27462106

Structures of mammalian ER α-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.

A.T.Caputo, D.S.Alonzi, L.Marti, I.B.Reca, J.L.Kiappes, W.B.Struwe, A.Cross, S.Basu, E.D.Lowe, B.Darlot, A.Santino, P.Roversi, N.Zitzmann.

ABSTRACT

The biosynthesis of enveloped viruses depends heavily on the host cell endoplasmic reticulum (ER) glycoprotein quality control (QC) machinery. This dependency exceeds the dependency of host glycoproteins, offering a window for the targeting of ERQC for the development of broad-spectrum antivirals. We determined small-angle X-ray scattering (SAXS) and crystal structures of the main ERQC enzyme, ER α-glucosidase II (α-GluII; from mouse), alone and in complex with key ligands of its catalytic cycle and antiviral iminosugars, including two that are in clinical trials for the treatment of dengue fever. The SAXS data capture the enzyme's quaternary structure and suggest a conformational rearrangement is needed for the simultaneous binding of a monoglucosylated glycan to both subunits. The X-ray structures with key catalytic cycle intermediates highlight that an insertion between the +1 and +2 subsites contributes to the enzyme's activity and substrate specificity, and reveal that the presence of d-mannose at the +1 subsite renders the acid catalyst less efficient during the cleavage of the monoglucosylated substrate. The complexes with iminosugar antivirals suggest that inhibitors targeting a conserved ring of aromatic residues between the α-GluII +1 and +2 subsites would have increased potency and selectivity, thus providing a template for further rational drug design.