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PDBsum entry 1qwn

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protein ligands metals links
Hydrolase PDB id
1qwn
Jmol
Contents
Protein chain
1014 a.a. *
Ligands
NAG
GUL
TRS
MPD
Metals
_ZN
Waters ×1034
* Residue conservation analysis
PDB id:
1qwn
Name: Hydrolase
Title: Golgi alpha-mannosidase ii covalent intermediate complex wit fluoro-gulosyl-fluoride
Structure: Alpha-mannosidase ii. Chain: a. Fragment: family 38 catalytic domain (residues 94-1108). Synonym: mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase golgi alpha-mannosidase ii, aman ii. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: alpha-man-ii or gmii or cg18474/cg18802/cg8139. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227.
Resolution:
1.20Å     R-factor:   0.175     R-free:   0.192
Authors: S.Numao,D.A.Kuntz,S.G.Withers,D.R.Rose
Key ref:
S.Numao et al. (2003). Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. J Biol Chem, 278, 48074-48083. PubMed id: 12960159 DOI: 10.1074/jbc.M309249200
Date:
02-Sep-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q24451  (MAN2_DROME) -  Alpha-mannosidase 2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1108 a.a.
1014 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* 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.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

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

 

 
DOI no: 10.1074/jbc.M309249200 J Biol Chem 278:48074-48083 (2003)
PubMed id: 12960159  
 
 
Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates.
S.Numao, D.A.Kuntz, S.G.Withers, D.R.Rose.
 
  ABSTRACT  
 
The family 38 golgi alpha-mannosidase II, thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate, is a clinically important enzyme involved in glycoprotein processing. The structure of three different covalent glycosyl-enzyme intermediates have been determined to 1.2-A resolution for the Golgi alpha-mannosidase II from Drosophila melanogaster by use of fluorinated sugar analogues, both with the wild-type enzyme and a mutant enzyme in which the acid/base catalyst has been removed. All these structures reveal sugar intermediates bound in a distorted 1S5 skew boat conformation. The similarity of this conformation with that of the substrate in the recently determined structure of the Michaelis complex of a beta-mannanase (Ducros, V. M. A., Zechel, D. L., Murshudov, G. N., Gilbert, H. J., Szabo, L., Stoll, D., Withers, S. G., and Davies, G. J. (2002) Angew. Chem. Int. Ed. Engl. 41, 2824-2827) suggests that these disparate enzymes have recruited common stereoelectronic features in evolving their catalytic mechanisms.
 
  Selected figure(s)  
 
Figure 2.
FIG. 2. a, stereo diagrams for the electron density map around the region of Asp-204 and the covalently bound sugar formed during the hydrolysis of 5FGulF by wt dGMII (covalent bond is not depicted). b, stereo diagrams for the structure of the covalent intermediate (green) formed during the hydrolysis of 5FGulF by the wt dGMII in relation to selected active site residues (yellow). For clarity, only those parts of the side chain from the C- atom onwards are shown. In the case of Arg-876, only the backbone atoms are shown. The covalent intermediate is shown in green with the arrow indicating the position of the new covalent bond.
Figure 3.
FIG. 3. Schematic of the interactions made by select active site residues and 5FGulF (a), deoxymannojirimycin (b), and swainsonine (c).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 48074-48083) copyright 2003.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19940122 A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, and S.C.Garman (2010).
Catalytic mechanism of human alpha-galactosidase.
  J Biol Chem, 285, 3625-3632.
PDB codes: 3hg2 3hg3 3hg4 3hg5
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.  
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
20081828 Y.Zhu, M.D.Suits, A.J.Thompson, S.Chavan, Z.Dinev, C.Dumon, N.Smith, K.W.Moremen, Y.Xiang, A.Siriwardena, S.J.Williams, H.J.Gilbert, and G.J.Davies (2010).
Mechanistic insights into a Ca2+-dependent family of alpha-mannosidases in a human gut symbiont.
  Nat Chem Biol, 6, 125-132.
PDB codes: 2wvx 2wvy 2wvz 2ww0 2ww1 2ww2 2ww3 2wzs
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
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18408714 L.E.Tailford, W.A.Offen, N.L.Smith, C.Dumon, C.Morland, J.Gratien, M.P.Heck, R.V.Stick, Y.Blériot, A.Vasella, H.J.Gilbert, and G.J.Davies (2008).
Structural and biochemical evidence for a boat-like transition state in beta-mannosidases.
  Nat Chem Biol, 4, 306-312.
PDB codes: 2vjx 2vl4 2vmf 2vo5 2vot 2vqt 2vqu 2vr4
18421285 M.M.Palcic (2008).
Beta-mannoside hydrolysis goes by boat.
  Nat Chem Biol, 4, 269-270.  
18076078 N.S.Kumar, D.A.Kuntz, X.Wen, B.M.Pinto, and D.R.Rose (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.
PDB codes: 2ow6 2ow7
18599462 N.Shah, D.A.Kuntz, and D.R.Rose (2008).
Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site.
  Proc Natl Acad Sci U S A, 105, 9570-9575.
PDB codes: 3cv5 3czn 3czs
17557336 P.Englebienne, H.Fiaux, D.A.Kuntz, C.R.Corbeil, S.Gerber-Lemaire, D.R.Rose, and N.Moitessier (2007).
Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.
  Proteins, 69, 160-176.
PDB codes: 2f18 2f1a 2f1b
16787095 S.P.Kawatkar, D.A.Kuntz, R.J.Woods, D.R.Rose, and G.J.Boons (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.
PDB codes: 2f7o 2f7p
16823793 V.A.Money, N.L.Smith, A.Scaffidi, R.V.Stick, H.J.Gilbert, and G.J.Davies (2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
  Angew Chem Int Ed Engl, 45, 5136-5140.
PDB codes: 2cip 2cit
16495121 V.L.Yip, and S.G.Withers (2006).
Breakdown of oligosaccharides by the process of elimination.
  Curr Opin Chem Biol, 10, 147-155.  
15800866 A.Siriwardena, H.Strachan, S.El-Daher, G.Way, B.Winchester, J.Glushka, K.Moremen, and G.J.Boons (2005).
Potent and selective inhibition of class II alpha-D-mannosidase activity by a bicyclic sulfonium salt.
  Chembiochem, 6, 845-848.  
15515081 F.Vincent, T.M.Gloster, J.Macdonald, C.Morland, R.V.Stick, F.M.Dias, J.A.Prates, C.M.Fontes, H.J.Gilbert, and G.J.Davies (2004).
Common inhibition of both beta-glucosidases and beta-mannosidases by isofagomine lactam reflects different conformational itineraries for pyranoside hydrolysis.
  Chembiochem, 5, 1596-1599.
PDB codes: 1uz1 1uz4
15062085 J.Allouch, W.Helbert, B.Henrissat, and M.Czjzek (2004).
Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.
  Structure, 12, 623-632.
PDB code: 1urx
15174846 J.Gonzalez-Outeiriño, J.Glushka, A.Siriwardena, and R.J.Woods (2004).
The structure and conformational behavior of sulfonium salt glycosidase inhibitors in solution: a combined quantum mechanical NMR approach.
  J Am Chem Soc, 126, 6866-6867.  
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.