5KK7

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase T688A mutant and Thio-disaccharide substrate analog complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7324 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


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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
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
A, B
455Homo sapiensMutation(s): 1 
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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PS
Query on 1PS

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A
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
1-(3-SULFOPROPYL) PYRIDINIUM, PPS
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
SMD
Query on SMD

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

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7324 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.887α = 105.68
b = 56.302β = 94.15
c = 89.555γ = 114.25
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release