Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with tunicamycin

Experimental Data Snapshot

  • Resolution: 3.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

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Ligand Structure Quality Assessment 

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Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance TB Antibiotic Design.

Dong, Y.Y.Wang, H.Pike, A.C.W.Cochrane, S.A.Hamedzadeh, S.Wyszynski, F.J.Bushell, S.R.Royer, S.F.Widdick, D.A.Sajid, A.Boshoff, H.I.Park, Y.Lucas, R.Liu, W.M.Lee, S.S.Machida, T.Minall, L.Mehmood, S.Belaya, K.Liu, W.W.Chu, A.Shrestha, L.Mukhopadhyay, S.M.M.Strain-Damerell, C.Chalk, R.Burgess-Brown, N.A.Bibb, M.J.Barry Iii, C.E.Robinson, C.V.Beeson, D.Davis, B.G.Carpenter, E.P.

(2018) Cell 175: 1045-1058.e16

  • DOI: https://doi.org/10.1016/j.cell.2018.10.037
  • Primary Citation of Related Structures:  
    5LEV, 5O5E, 6FM9, 6FWZ

  • PubMed Abstract: 

    Protein N-glycosylation is a widespread post-translational modification. The first committed step in this process is catalysed by dolichyl-phosphate N-acetylglucosamine-phosphotransferase DPAGT1 (GPT/E.C. Missense DPAGT1 variants cause congenital myasthenic syndrome and disorders of glycosylation. In addition, naturally-occurring bactericidal nucleoside analogues such as tunicamycin are toxic to eukaryotes due to DPAGT1 inhibition, preventing their clinical use. Our structures of DPAGT1 with the substrate UDP-GlcNAc and tunicamycin reveal substrate binding modes, suggest a mechanism of catalysis, provide an understanding of how mutations modulate activity (thus causing disease) and allow design of non-toxic "lipid-altered" tunicamycins. The structure-tuned activity of these analogues against several bacterial targets allowed the design of potent antibiotics for Mycobacterium tuberculosis, enabling treatment in vitro, in cellulo and in vivo, providing a promising new class of antimicrobial drug.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford, OX3 7DQ, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase409Homo 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9LH

Download Ideal Coordinates CCD File 
C [auth A]Tunicamycin
C38 H62 N4 O16
Query on P6L

Download Ideal Coordinates CCD File 
C40 H75 O10 P
Query on UNL

Download Ideal Coordinates CCD File 
D [auth A]Unknown ligand
Experimental Data & Validation

Experimental Data

  • Resolution: 3.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.091α = 90
b = 102.091β = 90
c = 240.061γ = 120
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
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references