6TS2 | pdb_00006ts2

Truncated version of Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) lacking domain TRXL2 (417-650).

PDB DOI: https://doi.org/10.2210/pdb6TS2/pdb

Classification: PROTEIN BINDING
Organism(s): Thermochaetoides thermophila DSM 1495
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-12-19 Released: 2020-01-08
Deposition Author(s): Roversi, P., Zitzmann, N.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 5.74 Å
R-Value Free:
0.249 (Depositor), 0.253 (DCC)
R-Value Work:
0.174 (Depositor), 0.184 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.4 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

PubMed: 33352114 Search on PubMed Search on PubMed Central
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.

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: marti.marcelo@gmail.com.

Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. Electronic address: nicole.zitzmann@bioch.ox.ac.uk.

Macromolecule Content

Total Structure Weight: 575.33 kDa
Atom Count: 36,079
Modeled Residue Count: 4,467
Deposited Residue Count: 5,040
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose-glycoprotein glucosyltransferase-like protein,UDP-glucose-glycoprotein glucosyltransferase-like protein	A, B, C, D	1,260	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SB58
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H	3		N-Glycosylation	Interactions Focus chain F Focus chain H Interactions & Density Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	4		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] M [auth B] N [auth B] I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain L [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A]	L [auth A], P [auth B], T [auth C], X [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 5.74 Å
R-Value Free: 0.249 (Depositor), 0.253 (DCC)
R-Value Work: 0.174 (Depositor), 0.184 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.145	α = 90
b = 191.014	β = 117.7
c = 158.807	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-08

Deposition Author(s):

Roversi, P.

Zitzmann, N.

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 (Full details and data files)

Version 1.0: 2020-01-08
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-01-13
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2021-04-14
Changes: Database references
Version 2.3: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 2.4: 2024-11-20
Changes: Structure summary