6TS8 | pdb_00006ts8

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

• PDB DOI: https://doi.org/10.2210/pdb6TS8/pdb

• Classification: PROTEIN BINDING
• Organism(s): Thermochaetoides thermophila DSM 1495
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2019-12-20 Released: 2020-10-28 
• Deposition Author(s): Roversi, P., Zitzmann, N., Ibba, R., Hensen, M., Chandran, A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.60 Å
• R-Value Free: 
  0.234 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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

• PubMed: 33352114 
• DOI: https://doi.org/10.1016/j.str.2020.11.017
• Primary Citation Related Structures: 
  6TRF, 6TRT, 6TS2, 6TS8, 9A0I


• 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). 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.

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Organizational Affiliation: 
• Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina.
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Dipartimento di Chimica e Farmacia, Università degli Studi di Sassari, Via Muroni 23A, 07100 Sassari, SS, Italy.
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.
Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy.
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; Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy.
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy.
Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET. Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina. Electronic address: [e-mail].
Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. Electronic address: [e-mail].
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 312.71 kDa 
• Atom Count: 20,112 
• Modeled Residue Count: 2,508 
• Deposited Residue Count: 2,764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose-glycoprotein glucosyltransferase-like protein	A, B	1,382	Thermochaetoides thermophila DSM 1495	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.60 Å
• R-Value Free:  0.234 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.047	α = 90
b = 139.047	β = 90
c = 176.091	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-28 
Deposition Author(s): Roversi, P., Zitzmann, N., Ibba, R., Hensen, M., Chandran, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	204801/Z/16/Z
Wellcome Trust	United Kingdom	106272/Z/14/Z
Wellcome Trust	United Kingdom	214090/Z/18/Z

Revision History  

• 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
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary