5KKB

Structure of mouse Golgi alpha-1,2-mannosidase IA and Man9GlcNAc2-PA complex

  • Classification: SUGAR BINDING PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Komagataella pastoris

  • Deposited: 2016-06-21 Released: 2016-12-07 
  • Deposition Author(s): Xiang, Y., Moremen, K.W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.774 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.

Xiang, Y.Karaveg, K.Moremen, K.W.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: E7890-E7899

  • DOI: 10.1073/pnas.1611213113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secr ...

    Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca2+ ion with a lanthanum (La3+) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La3+-bound enzymes with Man9GlcNAc2 substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA
A, B
469Mus musculusMutation(s): 0 
Gene Names: Man1a1 (Man1a)
EC: 3.2.1.113
Find proteins for P45700 (Mus musculus)
Go to UniProtKB:  P45700
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LA
Query on LA

Download SDF File 
Download CCD File 
A, B
LANTHANUM (III) ION
La
CZMAIROVPAYCMU-UHFFFAOYSA-N
 Ligand Interaction
1PS
Query on 1PS

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Download CCD File 
A, B
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
BU1
Query on BU1

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

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.774 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.955α = 90.00
b = 131.487β = 90.00
c = 87.785γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM047533
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK075322
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103390

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence