6TS8

Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant G177C/A786C.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase.

Modenutti, C.P.Blanco Capurro, J.I.Ibba, R.Alonzi, D.S.Song, M.N.Vasiljevic, S.Kumar, A.Chandran, A.V.Tax, G.Marti, L.Hill, J.C.Lia, A.Hensen, M.Waksman, T.Rushton, J.Rubichi, S.Santino, A.Marti, M.A.Zitzmann, N.Roversi, P.

(2021) Structure 29: 357

  • DOI: 10.1016/j.str.2020.11.017
  • Primary Citation of Related Structures:  
    6TRF, 6TRT, 6TS2, 6TS8

  • PubMed Abstract: 
  • UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2) ...

    UDP-glucose:glycoprotein glucosyltransferase (UGGT) flags misfolded glycoproteins for ER retention. We report crystal structures of full-length Chaetomium thermophilum UGGT (CtUGGT), two CtUGGT double-cysteine mutants, and its TRXL2 domain truncation (CtUGGT-ΔTRXL2). CtUGGT molecular dynamics (MD) simulations capture extended conformations and reveal clamping, bending, and twisting inter-domain movements. We name "Parodi limit" the maximum distance on the same glycoprotein between a site of misfolding and an N-linked glycan that can be reglucosylated by monomeric UGGT in vitro, in response to recognition of misfold at that site. Based on the MD simulations, we estimate the Parodi limit as around 70-80 Å. Frequency distributions of distances between glycoprotein residues and their closest N-linked glycosylation sites in glycoprotein crystal structures suggests relevance of the Parodi limit to UGGT activity in vivo. Our data support a "one-size-fits-all adjustable spanner" UGGT substrate recognition model, with an essential role for the UGGT TRXL2 domain.


    Organizational Affiliation

    Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH,, UK. Electronic address: pr159@leicester.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-glucose-glycoprotein glucosyltransferase-like proteinA, B1382Chaetomium thermophilum var. thermophilum DSM 1495Mutation(s): 2 
Gene Names: CTHT_0048990
UniProt
Find proteins for G0SB58 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SB58 
Go to UniProtKB:  G0SB58
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SB58
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.047α = 90
b = 139.047β = 90
c = 176.091γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom204801/Z/16/Z
Wellcome TrustUnited Kingdom106272/Z/14/Z
Wellcome TrustUnited Kingdom214090/Z/18/Z

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Database references
  • Version 1.2: 2021-04-14
    Changes: Database references