PDBsum entry: 2f7o

Hydrolase

PDB id: 2f7o

Contents

Protein chain

1014 a.a. *

Ligands

NAG

PO4

MSN

MPD

Metals

_ZN

Waters ×1048

* Residue conservation analysis

PDB id:

2f7o

Name:

Hydrolase

Title:

Golgi alpha-mannosidase ii complex with mannostatin a

Structure:

Alpha-mannosidase ii. Chain: a. Fragment: catalytic domain. Synonym: mannosyl-oligosaccharide 1,3-1,6- alpha-mannosidas golgi alpha-mannosidase ii. Aman ii. Engineered: yes

Source:

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

Resolution:

1.43Å R-factor: 0.206 R-free: 0.235

Authors:

D.A.Kuntz,D.R.Rose

Key ref:

S.P.Kawatkar et al. (2006). Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc, 128, 8310-8319. PubMed id: 16787095 DOI: 10.1021/ja061216p

Date:

01-Dec-05 Release date: 04-Jul-06

Protein chain

Q24451  (MAN2_DROME) -  Alpha-mannosidase 2

Seq: 1108 a.a.

Struc: 1014 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: 10.1021/ja061216p

J Am Chem Soc 128:8310-8319 (2006)

PubMed id: 16787095

Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions.

S.P.Kawatkar, D.A.Kuntz, R.J.Woods, D.R.Rose, G.J.Boons.

ABSTRACT

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi alpha-mannosidase II (dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E. In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements around the methionine residues in the protein. Collectively, our studies contradict the long held view that potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.