9N3S | pdb_00009n3s

Crystal structure of the fungal mannosyltransferase Och1 reveals active site primed for N-glycan binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: in silico
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Literature

Crystal structure of the fungal mannosyltransferase Och1 reveals active site primed for N-glycan binding.

Kelly, E.T.R.Rodionov, D.Sleno, B.Romero, P.A.Berghuis, A.M.

(2025) PLoS One 20: e0329259-e0329259

  • DOI: https://doi.org/10.1371/journal.pone.0329259
  • Primary Citation of Related Structures:  
    9N3S

  • PubMed Abstract: 

    The outermost layer of a fungi's cell wall serves as the organism's point of first contact with its environment, or host. Heavily glycosylated glycoproteins anchor a complex meshwork of branching mannose chains, forming the outer cell wall layer in most yeast and mold species. Outer mannan chains are composed of large polymannose branching glycans attached to the universal eukaryotic N-glycan GlcNAc2Man8 core. Synthesized in the endoplasmic reticulum, the core N-glycan is transferred to the Golgi apparatus, where the first fungi-specific reaction takes place. In the cis-Golgi, Och1 (Outer chain elongation 1) plays a central role in initiating outer mannan cell wall synthesis by transferring a single α-1,6-mannose residue to the N-GlcNAc2Man8 core. Playing a vital role in fungal biology, fungal cell wall synthesis proteins have long since been thought as attractive options in the search for a fungi-specific drug target. Saccharomyces cerevisiae Δ52-Och1 was expressed in Pichia pastoris. Here, the first X-ray crystal structure of a fungal Och1 protein is reported, determined to 2.0 Å. Molecular modeling of ligand binding and sequence analysis has revealed a highly conserved substrate binding site, rationalizing Och1 target specificity for the N-GlcNAc2Man8 glycan.


  • Organizational Affiliation
    • Department of Biochemistry, McGill University, Montréal, Québec, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Initiation-specific alpha-1,6-mannosyltransferase
A, B
431Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OCH1NGD29YGL038C
EC: 2.4.1.232
UniProt
Find proteins for P31755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31755 
Go to UniProtKB:  P31755
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31755
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P31755-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42227JK
GlyCosmos:  G42227JK
GlyGen:  G42227JK
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD
GlyCosmos:  G81315DD
GlyGen:  G81315DD
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.447α = 85.57
b = 57.09β = 75.31
c = 84.088γ = 75.13
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-114889
Canadian Institutes of Health Research (CIHR)CanadaPJT-162365

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release