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PDBsum entry 1x9d

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protein ligands metals links
Hydrolase PDB id
1x9d
Jmol
Contents
Protein chain
452 a.a. *
Ligands
SO4
SMD
BU1
Metals
_CA
Waters ×376
* Residue conservation analysis
PDB id:
1x9d
Name: Hydrolase
Title: Crystal structure of human class i alpha-1,2-mannosidase in complex with thio-disaccharide substrate analogue
Structure: Endoplasmic reticulum mannosyl-oligosaccharide 1, 2-alpha-mannosidase. Chain: a. Fragment: residues 243-699. Synonym: er alpha-1,2-mannosidase, mannosidase alpha class 1b member 1, man9glcnac2-specific processing alpha- mannosidase, unq747/pro1477. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: man1b1. Expressed in: pichia pastoris. Expression_system_taxid: 4922
Resolution:
1.41Å     R-factor:   0.146     R-free:   0.162
Authors: K.Karaveg,W.Tempel,Z.J.Liu,A.Siriwardena,K.W.Moremen, B.C.Wang
Key ref:
K.Karaveg et al. (2005). Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control. J Biol Chem, 280, 16197-16207. PubMed id: 15713668 DOI: 10.1074/jbc.M500119200
Date:
20-Aug-04     Release date:   22-Feb-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UKM7  (MA1B1_HUMAN) -  Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
Seq:
Struc:
 
Seq:
Struc:
699 a.a.
452 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.113  - Mannosyl-oligosaccharide 1,2-alpha-mannosidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biochemical function     calcium ion binding     2 terms  

 

 
DOI no: 10.1074/jbc.M500119200 J Biol Chem 280:16197-16207 (2005)
PubMed id: 15713668  
 
 
Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.
K.Karaveg, A.Siriwardena, W.Tempel, Z.J.Liu, J.Glushka, B.C.Wang, K.W.Moremen.
 
  ABSTRACT  
 
Quality control in the endoplasmic reticulum (ER) determines the fate of newly synthesized glycoproteins toward either correct folding or disposal by ER-associated degradation. Initiation of the disposal process involves selective trimming of N-glycans attached to misfolded glycoproteins by ER alpha-mannosidase I and subsequent recognition by the ER degradation-enhancing alpha-mannosidase-like protein family of lectins, both members of glycosylhydrolase family 47. The unusual inverting hydrolytic mechanism catalyzed by members of this family is investigated here by a combination of kinetic and binding analyses of wild type and mutant forms of human ER alpha-mannosidase I as well as by structural analysis of a co-complex with an uncleaved thiodisaccharide substrate analog. These data reveal the roles of potential catalytic acid and base residues and the identification of a novel (3)S(1) sugar conformation for the bound substrate analog. The co-crystal structure described here, in combination with the (1)C(4) conformation of a previously identified co-complex with the glycone mimic, 1-deoxymannojirimycin, indicates that glycoside bond cleavage proceeds through a least motion conformational twist of a properly predisposed substrate in the -1 subsite. A novel (3)H(4) conformation is proposed as the exploded transition state.
 
  Selected figure(s)  
 
Figure 5.
FIG. 5. Normalized F[o] - F[c] disaccharide electron density map for the thioin the active site of ERManI and comparison of the sugar ring conformations with the enzyme-bound conformation of dMNJ in the -1 subsite and the M7 mannose residue in the +1 subsite. A, a stereographic representation of the difference electron density for the omitted inhibitor in the ERManI-thiodisaccharide cocomplex. The inhibitor model is shown to aid in map interpretation. The reducing terminal Man- -O-CH[3] is shown at the top, labeled as the +1 subsite residue, and the nonreducing terminal Man residue in the 3S[1] conformation is labeled as the -1 subsite residue. Carbon and sulfur atoms in the structures are labeled as a reference. The electron density map was contoured at 3 for the gray mesh and 10 for the red mesh, demonstrating the significant electron density at the glycosidic sulfur, the O-3' and O-4' hydroxyls of the +1 residue, and the O-2', O-3', and O-4' hydroxyls of the -1 residue. B, the protein structure of the ER-ManI-thiodisaccharide co-complex was aligned with the corresponding protein structures of the ERManI·dMNJ co-complex (20) and the co-complex of yeast ERManI containing a Man[5]GlcNAc[2] glycan in the active site (21) using Swiss-PdbViewer (version 3.7) (55). Displayed in the figure are the structures of the thiodisaccharide (yellow stick figure), dMNJ (green stick figure), and the M7 residue of the Man[5]GlcNAc[2] glycan in the +1 subsite (white stick figure; see Ref. 19 for oligosaccharide residue nomenclature). Carbon and sulfur atoms in the structures are labeled as a reference. The M7 residue is in an identical conformation as the +1 residue of the thiodisaccharide and in a similar position except for an offset of 0.5-0.7 Å resulting from the longer C-S bond lengths of the thiodisaccharide. The positioning of the -1 subsite residues (dMNJ versus the -1 residue of the thiodisaccharide) were virtually identical at the C-2, C-3, and C-4 positions. The main differences between the two structures were found in the equivalent of the C-1, O-5, C-5, and C-6 positions.
Figure 7.
FIG. 7. Interactions between the thiodisaccharide and the +1 and -1 binding sites in human ERManI. Shown is a schematic diagram (left panel) of the interactions between the thiodisaccharide and ERManI in the -1 and +1 subsites, demonstrating hydrogen bonding interactions (green dotted lines), direct coordination of the enzyme-associated Ca^2+ ion (blue dotted lines), hydrophobic stacking of Phe^659 with the C-4-C-5-C-6 region of the -1 residue (black dotted lines), and proposed acid-catalyzed through-water (W8) protonation of the glycosidic oxygen (sulfur in the thiodisaccharide) and the base-catalyzed (Glu599) attack by the water nucleophile (W5) (red dotted lines). Residue numbering of amino acid side chains in the respective subsites is indicated. The stereo view (center and right) illustrates a stick diagram of the interaction between the thiodisaccharide residues in the -1 and +1 subsites relative to the residues examined by mutagenesis here. Coordination to the Ca^2+ ion (blue dotted lines), and the proposed nucleophile trajectory and acid protonation of the glycosidic oxygen (red dotted lines) are indicated. The small red and green space fill structures representing the water molecules and carbonyl oxygen and O- of Thr688 that coordinate the Ca^2+ ion are as described in the legend to Fig. 2. The green dotted lines indicate hydrogen bonds between the respective residues.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 16197-16207) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19853458 M.Aebi, R.Bernasconi, S.Clerc, and M.Molinari (2010).
N-glycan structures: recognition and processing in the ER.
  Trends Biochem Sci, 35, 74-82.  
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
20552664 T.V.Vuong, and D.B.Wilson (2010).
Glycoside hydrolases: catalytic base/nucleophile diversity.
  Biotechnol Bioeng, 107, 195-205.  
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
19524542 J.H.Cormier, T.Tamura, J.C.Sunryd, and D.N.Hebert (2009).
EDEM1 recognition and delivery of misfolded proteins to the SEL1L-containing ERAD complex.
  Mol Cell, 34, 627-633.  
19621226 J.Zhou, C.Z.Lin, X.Z.Zheng, X.J.Lin, W.J.Sang, S.H.Wang, Z.H.Wang, D.Ebbole, and G.D.Lu (2009).
Functional analysis of an alpha-1,2-mannosidase from Magnaporthe oryzae.
  Curr Genet, 55, 485-496.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
17588125 H.M.Mora-Montes, E.López-Romero, S.Zinker, P.Ponce-Noyola, and A.Flores-Carreón (2008).
Conversion of alpha1,2-mannosidase E-I from Candida albicans to alpha1,2-mannosidase E-II by limited proteolysis.
  Antonie Van Leeuwenhoek, 93, 61-69.  
18706423 K.N.Beverly, M.R.Sawaya, E.Schmid, and C.M.Koehler (2008).
The Tim8-Tim13 complex has multiple substrate binding sites and binds cooperatively to Tim23.
  J Mol Biol, 382, 1144-1156.
PDB code: 3cjh
17849372 K.N.Kirschner, A.B.Yongye, S.M.Tschampel, J.González-Outeiriño, C.R.Daniels, B.L.Foley, and R.J.Woods (2008).
GLYCAM06: A generalizable biomolecular force field. Carbohydrates.
  J Comput Chem, 29, 622-655.  
18848471 T.M.Gloster, J.P.Turkenburg, J.R.Potts, B.Henrissat, and G.J.Davies (2008).
Divergence of catalytic mechanism within a glycosidase family provides insight into evolution of carbohydrate metabolism by human gut flora.
  Chem Biol, 15, 1058-1067.
PDB codes: 2jka 2jke 2jkp
18323617 Y.D.Lobsanov, T.Yoshida, T.Desmet, W.Nerinckx, P.Yip, M.Claeyssens, A.Herscovics, and P.L.Howell (2008).
Modulation of activity by Arg407: structure of a fungal alpha-1,2-mannosidase in complex with a substrate analogue.
  Acta Crystallogr D Biol Crystallogr, 64, 227-236.
PDB codes: 2ri8 2ri9
17510649 M.Molinari (2007).
N-glycan structure dictates extension of protein folding or onset of disposal.
  Nat Chem Biol, 3, 313-320.  
17906960 P.Marchetti, M.Bugliani, R.Lupi, L.Marselli, M.Masini, U.Boggi, F.Filipponi, G.C.Weir, D.L.Eizirik, and M.Cnop (2007).
The endoplasmic reticulum in pancreatic beta cells of type 2 diabetes patients.
  Diabetologia, 50, 2486-2494.  
17125150 R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.
  J Mol Recognit, 19, 478-534.  
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
16115860 C.Park, L.Meng, L.H.Stanton, R.E.Collins, S.W.Mast, X.Yi, H.Strachan, and K.W.Moremen (2005).
Characterization of a human core-specific lysosomal {alpha}1,6-mannosidase involved in N-glycan catabolism.
  J Biol Chem, 280, 37204-37216.  
15939591 D.N.Hebert, S.C.Garman, and M.Molinari (2005).
The glycan code of the endoplasmic reticulum: asparagine-linked carbohydrates as protein maturation and quality-control tags.
  Trends Cell Biol, 15, 364-370.  
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.