5MU1

UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum soaked with K2PtI6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint.

Roversi, P.Marti, L.Caputo, A.T.Alonzi, D.S.Hill, J.C.Dent, K.C.Kumar, A.Levasseur, M.D.Lia, A.Waksman, T.Basu, S.Soto Albrecht, Y.Qian, K.McIvor, J.P.Lipp, C.B.Siliqi, D.Vasiljevic, S.Mohammed, S.Lukacik, P.Walsh, M.A.Santino, A.Zitzmann, N.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 8544-8549

  • DOI: 10.1073/pnas.1703682114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glycoproteins traversing the eukaryotic secretory pathway begin life in the endoplasmic reticulum (ER), where their folding is surveyed by the 170-kDa UDP-glucose:glycoprotein glucosyltransferase (UGGT). The enzyme acts as the single glycoprotein fol ...

    Glycoproteins traversing the eukaryotic secretory pathway begin life in the endoplasmic reticulum (ER), where their folding is surveyed by the 170-kDa UDP-glucose:glycoprotein glucosyltransferase (UGGT). The enzyme acts as the single glycoprotein folding quality control checkpoint: it selectively reglucosylates misfolded glycoproteins, promotes their association with ER lectins and associated chaperones, and prevents premature secretion from the ER. UGGT has long resisted structural determination and sequence-based domain boundary prediction. Questions remain on how this single enzyme can flag misfolded glycoproteins of different sizes and shapes for ER retention and how it can span variable distances between the site of misfold and a glucose-accepting N-linked glycan on the same glycoprotein. Here, crystal structures of a full-length eukaryotic UGGT reveal four thioredoxin-like (TRXL) domains arranged in a long arc that terminates in two β-sandwiches tightly clasping the glucosyltransferase domain. The fold of the molecule is topologically complex, with the first β-sandwich and the fourth TRXL domain being encoded by nonconsecutive stretches of sequence. In addition to the crystal structures, a 15-Å cryo-EM reconstruction reveals interdomain flexibility of the TRXL domains. Double cysteine point mutants that engineer extra interdomain disulfide bridges rigidify the UGGT structure and exhibit impaired activity. The intrinsic flexibility of the TRXL domains of UGGT may therefore endow the enzyme with the promiscuity needed to recognize and reglucosylate its many different substrates and/or enable reglucosylation of N-linked glycans situated at variable distances from the site of misfold.


    Organizational Affiliation

    Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; pietro.roversi@bioch.ox.ac.uk nicole.zitzmann@bioch.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-glucose-glycoprotein glucosyltransferase-like protein
A
1494Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0SB58 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0SB58
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PT
Query on PT

Download SDF File 
Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.237 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 116.950α = 90.00
b = 116.950β = 90.00
c = 301.491γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
Aimlessdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom097300/Z/11/Z
Wellcome TrustUnited Kingdom106272/Z/14/Z

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Database references