PDBsum entry: 2ow6

Hydrolase

PDB id: 2ow6

Contents

Protein chain

1016 a.a. *

Ligands

NAG

PO4 ×2

NK1

MRD

Metals

_ZN

Waters ×1466

* Residue conservation analysis

PDB id:

2ow6

Name:

Hydrolase

Title:

Golgi alpha-mannosidase ii complex with (1r,5s,6s,7r,8s)-1- thioniabicyclo[4.3.0]nonan-5,7,8-triol chloride

Structure:

Alpha-mannosidase 2. Chain: a. Fragment: catalytic domain (residues 76-1108). Synonym: alpha-mannosidase ii, mannosyl- oligosaccharide 1, alpha-mannosidase, man ii, golgi alpha- mannosidase ii, ama engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: alpha-man-ii. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227.

Resolution:

1.19Å R-factor: 0.118 R-free: 0.150

Authors:

D.A.Kuntz

Key ref:

N.S.Kumar et al. (2008). Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: The role of water in inhibitor binding. Proteins, 71, 1484-1496. PubMed id: 18076078 DOI: 10.1002/prot.21850

Date:

15-Feb-07 Release date: 08-Jan-08

Protein chain

Q24451  (MAN2_DROME) -  Alpha-mannosidase 2

Seq: 1108 a.a.

Struc: 1016 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.114 - Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase.
• Pathway: Mannosyl-glycoprotein N-acetylglucosaminyltransferases
• Reaction: Hydrolysis of the terminal 1,3- and 1,6-linked alpha-D-mannose residues in the mannosyl-oligosaccharide Man(5)(GlcNAc)(3).

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (6 terms)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (11 terms)

DOI no: 10.1002/prot.21850

Proteins 71:1484-1496 (2008)

PubMed id: 18076078

Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: The role of water in inhibitor binding.

N.S.Kumar, D.A.Kuntz, X.Wen, B.M.Pinto, D.R.Rose.

ABSTRACT

Retaining glycosidases operate by a two-step catalytic mechanism in which the transition states are characterized by buildup of a partial positive charge at the anomeric center. Sulfonium-ion analogues of the naturally occurring glycosidase inhibitors, swainsonine and 8-epi-lentiginosine, in which the bridgehead nitrogen atom is replaced by a sulfonium-ion, were synthesized in order to test the hypothesis that a sulfonium salt carrying a permanent positive charge would be an effective glycosidase inhibitor. Initial prediction based on computational docking indicated three plausible binding modes to Drosophila Golgi alpha-mannosidase II (dGMII), the most likely being close to that of swainsonine. Observation of the binding of di-epi-thioswainsonine and 8-epi-thiolentiginosine to dGMII from crystallographic data, however, revealed an orientation different from swainsonine in the active site. Screening these two compounds against dGMII shows that they are inhibitors with IC(50) values of 2.0 and 0.014 mM, respectively. This dramatic difference in affinity between the two compounds, which differ by only one hydroxyl group, is rationalized in terms of bound water molecules and the water molecule substructure in the active site, as identified by comparison of high resolution X-ray crystal structures of several dGMII-inhibitor complexes.

Selected figure(s)

Figure 1.
Figure 1. Three predicted binding modes of compound 16 in the active site of dGMII from docking calculations: The zinc ion is shown as a magenta ball and the relevant side-chains as sticks. The calculated structure is superimposed on the crystal structure of swainsonine (6, pink) in the active site of dGMII.

Figure 6.
Figure 6. Comparison of electron density in the region around Arg228. The presence of water density at the position of Wat467 in the 17 structure (top) and its absence in the 16 structure bottom is unambiguous. The electron density is a 2Fobs-Fcalc map contoured at 1 sigma.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 71, 1484-1496) copyright 2008.

Figures were selected by an automated process.