6BW6

Human GPT (DPAGT1) H129 variant in complex with tunicamycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1038/s41594-018-0031-y
  • Primary Citation of Related Structures:  

  • 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-acetylglucosaminephosphotransf ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
A, B, C, D
417Homo sapiensMutation(s): 0 
Gene Names: DPAGT1 (DPAGT2)
EC: 2.7.8.15
Find proteins for Q9H3H5 (Homo sapiens)
Go to Gene View: DPAGT1
Go to UniProtKB:  Q9H3H5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TUM
Query on TUM

Download SDF File 
Download CCD File 
A, B, C, D
Tunicamycin
C37 H60 N4 O16
YJQCOFNZVFGCAF-DCSBULBVSA-N
 Ligand Interaction
PGW
Query on PGW

Download SDF File 
Download CCD File 
A, B, C
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)]; PHOSPHATIDYLGLYCEROL
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.260 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 210.615α = 90.00
b = 105.363β = 103.49
c = 148.080γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM120594
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR35NS097241

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Type: Author supporting evidence
  • Version 1.2: 2018-03-14
    Type: Database references
  • Version 1.3: 2018-03-21
    Type: Database references