7LOU

Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine

PDB DOI: https://doi.org/10.2210/pdb7LOU/pdb

Classification: TRANSFERASE/Inhibitor
Organism(s): Clostridioides difficile
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-10 Released: 2021-11-17
Deposition Author(s): Harijan, R.K., Paparella, A.S., Aboulache, B.L., Bonanno, J.B., Almo, S.C., Schramm, V.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.252
R-Value Work: 0.215
R-Value Observed: 0.217

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues.

Paparella, A.S., Aboulache, B.L., Harijan, R.K., Potts, K.S., Tyler, P.C., Schramm, V.L.

(2021) Nat Commun 12: 6285-6285

PubMed: 34725358 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-26580-6
Primary Citation of Related Structures:
7LOU, 7LOV

PubMed Abstract:
Clostridium difficile causes life-threatening diarrhea and is the leading cause of healthcare-associated bacterial infections in the United States. TcdA and TcdB bacterial toxins are primary determinants of disease pathogenesis and are attractive therapeutic targets. TcdA and TcdB contain domains that use UDP-glucose to glucosylate and inactivate host Rho GTPases, resulting in cytoskeletal changes causing cell rounding and loss of intestinal integrity. Transition state analysis revealed glucocationic character for the TcdA and TcdB transition states. We identified transition state analogue inhibitors and characterized them by kinetic, thermodynamic and structural analysis. Iminosugars, isofagomine and noeuromycin mimic the transition state and inhibit both TcdA and TcdB by forming ternary complexes with Tcd and UDP, a product of the TcdA- and TcdB-catalyzed reactions. Both iminosugars prevent TcdA- and TcdB-induced cytotoxicity in cultured mammalian cells by preventing glucosylation of Rho GTPases. Iminosugar transition state analogues of the Tcd toxins show potential as therapeutics for C. difficile pathology.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.

Macromolecule Content

Total Structure Weight: 131.02 kDa
Atom Count: 9,489
Modelled Residue Count: 1,085
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyltransferase TcdB	A, B	552	Clostridioides difficile	Mutation(s): 0 Gene Names: tcdB, toxB EC: 2.4.1 (PDB Primary Data), 3.4.22 (UniProt)
UniProt
Find proteins for P18177 (Clostridioides difficile) Explore P18177 Go to UniProtKB: P18177
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18177
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Y [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth B]	L [auth A], Y [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain L [auth A] Focus chain Y [auth B] Interactions & Density Focus chain L [auth A] Focus chain Y [auth B]
IFM (Subject of Investigation/LOI) Query on IFM Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Z [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Z [auth B]	M [auth A], Z [auth B]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C₆ H₁₃ N O₃ QPYJXFZUIJOGNX-HSUXUTPPSA-N		Interactions Focus chain M [auth A] Focus chain Z [auth B] Interactions & Density Focus chain M [auth A] Focus chain Z [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain E [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain E [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain E [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain N [auth A]	AA [auth B], N [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A]