1X9D

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control.

Karaveg, K.Siriwardena, A.Tempel, W.Liu, Z.J.Glushka, J.Wang, B.C.Moremen, K.W.

(2005) J.Biol.Chem. 280: 16197-16207

  • DOI: 10.1074/jbc.M500119200

  • PubMed 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-glyca ...

    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.


    Organizational Affiliation

    Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
A
538Homo sapiensMutation(s): 0 
Gene Names: MAN1B1
EC: 3.2.1.113
Find proteins for Q9UKM7 (Homo sapiens)
Go to Gene View: MAN1B1
Go to UniProtKB:  Q9UKM7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SMD
Query on SMD

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Download CCD File 
A
METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE
C13 H24 O10 S
WAYOKHSZGNFKSX-ZEEOCKJESA-N
 Ligand Interaction
BU1
Query on BU1

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Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SMDKd: 110000 nM BINDINGMOAD
SMDKd: 110000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 50.687α = 89.49
b = 53.878β = 63.60
c = 56.234γ = 62.61
Software Package:
Software NamePurpose
DENZOdata reduction
EPMRphasing
SCALEPACKdata scaling
MAR345data collection
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description