Human GPT (DPAGT1) H129 variant in complex with tunicamycin

Experimental Data Snapshot

  • Resolution: 2.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 

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Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


GlcNAc-1-P-transferase-tunicamycin complex structure reveals basis for inhibition of N-glycosylation.

Yoo, J.Mashalidis, E.H.Kuk, A.C.Y.Yamamoto, K.Kaeser, B.Ichikawa, S.Lee, S.Y.

(2018) Nat Struct Mol Biol 25: 217-224

  • DOI: https://doi.org/10.1038/s41594-018-0031-y
  • Primary Citation of Related Structures:  
    6BW5, 6BW6

  • PubMed Abstract: 

    N-linked glycosylation is a predominant post-translational modification of protein in eukaryotes, and its dysregulation is the etiology of several human disorders. The enzyme UDP-N-acetylglucosamine:dolichyl-phosphate N-acetylglucosaminephosphotransferase (GlcNAc-1-P-transferase or GPT) catalyzes the first and committed step of N-linked glycosylation in the endoplasmic reticulum membrane, and it is the target of the natural product tunicamycin. Tunicamycin has potent antibacterial activity, inhibiting the bacterial cell wall synthesis enzyme MraY, but its usefulness as an antibiotic is limited by off-target inhibition of human GPT. Our understanding of how tunicamycin inhibits N-linked glycosylation and efforts to selectively target MraY are hampered by a lack of structural information. Here we present crystal structures of human GPT in complex with tunicamycin. Structural and functional analyses reveal the difference between GPT and MraY in their mechanisms of inhibition by tunicamycin. We demonstrate that this difference could be exploited to design MraY-specific inhibitors as potential antibiotics.

  • Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
A, B, C, D
417Homo sapiensMutation(s): 1 
Gene Names: DPAGT1DPAGT2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3H5 (Homo sapiens)
Explore Q9H3H5 
Go to UniProtKB:  Q9H3H5
GTEx:  ENSG00000172269 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3H5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.261 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.615α = 90
b = 105.363β = 103.49
c = 148.08γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120594
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR35NS097241

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2018-03-21
    Changes: Database references
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description