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Hydrolase PDB id
1ps3
Jmol
Contents
Protein chain
1014 a.a. *
Ligands
NAG
KIF
MRD
Metals
_ZN
Waters ×983
* Residue conservation analysis
PDB id:
1ps3
Name: Hydrolase
Title: Golgi alpha-mannosidase ii in complex with kifunensine
Structure: Alpha-mannosidase ii. Chain: a. Synonym: mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase golgi alpha-mannosidase ii, aman ii. Ec: 3.2.1.114
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Cell_line: s2 cells
Resolution:
1.80Å     R-factor:   0.200     R-free:   0.222
Authors: N.Shah,D.A.Kuntz,D.R.Rose
Key ref:
N.Shah et al. (2003). Comparison of kifunensine and 1-deoxymannojirimycin binding to class I and II alpha-mannosidases demonstrates different saccharide distortions in inverting and retaining catalytic mechanisms. Biochemistry, 42, 13812-13816. PubMed id: 14636047 DOI: 10.1021/bi034742r
Date:
20-Jun-03     Release date:   16-Dec-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  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   3 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
DOI no: 10.1021/bi034742r Biochemistry 42:13812-13816 (2003)
PubMed id: 14636047  
 
 
Comparison of kifunensine and 1-deoxymannojirimycin binding to class I and II alpha-mannosidases demonstrates different saccharide distortions in inverting and retaining catalytic mechanisms.
N.Shah, D.A.Kuntz, D.R.Rose.
 
  ABSTRACT  
 
Mannosidases are key enzymes in the eukaryotic N-glycosylation pathway. These enzymes fall into two broad classes (I and II) and are characteristically different in catalytic mechanism, sequence, and structure. Kifunensine is an alkaloid that is a strong inhibitor against class I alpha-mannosidases but is only a weak inhibitor against class II alpha-mannosidases. In this paper, the 1.80 A resolution crystal structure of kifunensine bound to Drosophila melanogaster Golgi alpha-mannosidase II (dGMII) is presented. Kifunensine adopts a (1,4)B boat conformation in the class II dGMII, which contrasts the (1)C(4) chair conformation seen in class I human endoplasmic reticulum alpha1,2 mannosidase (hERMI, PDB ). The observed conformations are higher in conformational energy than the global minimum (4)C(1) conformation, although the conformation in hERMI is closer to the minimum, as supported by an energy calculation. Differing conformations of 1-deoxymannojirimycin were also observed: a (4)C(1) and (1)C(4) conformation in dGMII and hERMI, respectively. Thus, these two alpha-mannosidase classes distort these inhibitors in distinct manners. This is likely indicative of the binding characteristics of the two different catalytic mechanisms of these enzymes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
18788072 D.J.Harvey, K.Baruah, and C.N.Scanlan (2009).
Application of negative ion MS/MS to the identification of N-glycans released from carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1).
  J Mass Spectrom, 44, 50-60.  
19208259 Y.Zhang, D.A.Rodionov, M.S.Gelfand, and V.N.Gladyshev (2009).
Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.
  BMC Genomics, 10, 78.  
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.  
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
15466477 R.P.Hughey, J.B.Bruns, C.L.Kinlough, and T.R.Kleyman (2004).
Distinct pools of epithelial sodium channels are expressed at the plasma membrane.
  J Biol Chem, 279, 48491-48494.  
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.