5LEV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1016/j.cell.2018.10.037
  • Primary Citation of Related Structures:  
    6FM9, 5O5E, 5LEV, 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. 2.7.8.15). Missense DPAGT1 variants cause congenital myasthenic syndrome and disorders of glycosylation ...

    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. 2.7.8.15). 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. Electronic address: liz.carpenter@sgc.ox.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferaseA409Homo sapiensMutation(s): 1 
Gene Names: DPAGT1DPAGT2
EC: 2.7.8.15
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3H5 (Homo sapiens)
Explore Q9H3H5 
Go to UniProtKB:  Q9H3H5
PHAROS:  Q9H3H5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNL
Query on UNL

Download Ideal Coordinates CCD File 
B [auth A]Unknown ligand
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.235 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.25α = 90
b = 103.25β = 90
c = 239.15γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092809/Z/10/Z

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references