PDBsum entry 3czn

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Protein chain
1014 a.a. *
Waters ×1158
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Golgi alpha-mannosidase ii (d204a nucleophile mutant) in com gnman5gn
Structure: Alpha-mannosidase 2. Chain: a. Fragment: catalytic domain. Unp residues 76-1108. Synonym: alpha-mannosidase ii, mannosyl-oligosaccharide 1,3 alpha-mannosidase, man ii, golgi alpha-mannosidase ii, aman engineered: yes. Mutation: yes
Source: Drosophila melanogaster. Fruit fly. Gene: alpha-man-ii, gmii. Expressed in: drosophila melanogaster.
1.40Å     R-factor:   0.178     R-free:   0.197
Authors: N.Shah,D.R.Rose
Key ref: N.Shah et al. (2008). Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site. Proc Natl Acad Sci U S A, 105, 9570-9575. PubMed id: 18599462
29-Apr-08     Release date:   24-Jun-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q24451  (MAN2_DROME) -  Alpha-mannosidase 2
1108 a.a.
1014 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

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 
  GO annot!
  Cellular component     membrane   6 terms 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     10 terms  


Proc Natl Acad Sci U S A 105:9570-9575 (2008)
PubMed id: 18599462  
Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site.
N.Shah, D.A.Kuntz, D.R.Rose.
Golgi alpha-mannosidase II (GMII) is a key glycosyl hydrolase in the N-linked glycosylation pathway. It catalyzes the removal of two different mannosyl linkages of GlcNAcMan(5)GlcNAc(2), which is the committed step in complex N-glycan synthesis. Inhibition of this enzyme has shown promise in certain cancers in both laboratory and clinical settings. Here we present the high-resolution crystal structure of a nucleophile mutant of Drosophila melanogaster GMII (dGMII) bound to its natural oligosaccharide substrate and an oligosaccharide precursor as well as the structure of the unliganded mutant. These structures allow us to identify three sugar-binding subsites within the larger active site cleft. Our results allow for the formulation of the complete catalytic process of dGMII, which involves a specific order of bond cleavage, and a major substrate rearrangement in the active site. This process is likely conserved for all GMII enzymes-but not in the structurally related lysosomal mannosidase-and will form the basis for the design of specific inhibitors against GMII.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20209559 D.A.Kuntz, S.Nakayama, K.Shea, H.Hori, Y.Uto, H.Nagasawa, and D.R.Rose (2010).
Structural investigation of the binding of 5-substituted swainsonine analogues to Golgi alpha-mannosidase II.
  Chembiochem, 11, 673-680.
PDB codes: 3ejp 3ejq 3ejr 3ejs 3ejt 3eju
20026005 D.J.Coleman, D.A.Kuntz, M.Venkatesan, G.M.Cook, S.P.Williamson, D.R.Rose, and J.J.Naleway (2010).
A long-wavelength fluorescent substrate for continuous fluorometric determination of alpha-mannosidase activity: resorufin alpha-D-mannopyranoside.
  Anal Biochem, 399, 7.  
20688784 D.Rendić, M.Sharrow, T.Katoh, B.Overcarsh, K.Nguyen, J.Kapurch, K.Aoki, I.B.Wilson, and M.Tiemeyer (2010).
Neural-specific α3-fucosylation of N-linked glycans in the Drosophila embryo requires fucosyltransferase A and influences developmental signaling associated with O-glycosylation.
  Glycobiology, 20, 1353-1365.  
20140249 M.D.Suits, Y.Zhu, E.J.Taylor, J.Walton, D.L.Zechel, H.J.Gilbert, and G.J.Davies (2010).
Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase.
  PLoS One, 5, e9006.
PDB codes: 2wyh 2wyi
19101978 D.A.Kuntz, W.Zhong, J.Guo, D.R.Rose, and G.J.Boons (2009).
The Molecular Basis of Inhibition of Golgi alpha-Mannosidase II by Mannostatin A.
  Chembiochem, 10, 268-277.
PDB codes: 3dx0 3dx1 3dx2 3dx3 3dx4
19465480 M.Crispin, V.T.Chang, D.J.Harvey, R.A.Dwek, E.J.Evans, D.I.Stuart, E.Y.Jones, J.M.Lord, R.A.Spooner, and S.J.Davis (2009).
A human embryonic kidney 293T cell line mutated at the Golgi alpha-mannosidase II locus.
  J Biol Chem, 284, 21684-21695.  
19722277 M.Venkatesan, D.A.Kuntz, and D.R.Rose (2009).
Human lysosomal alpha-mannosidases exhibit different inhibition and metal binding properties.
  Protein Sci, 18, 2242-2251.  
19756298 R.D.Cummings (2009).
The repertoire of glycan determinants in the human glycome.
  Mol Biosyst, 5, 1087-1104.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.