8QMF

Transketolase from Vibrio vulnificus in complex with thiamin pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb8QMF/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Vibrio vulnificus YJ016
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-22 Released: 2024-02-07
Deposition Author(s): Ballut, L., Georges, R.N., Octobre, G., Charmantray, F., Doumeche, B.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.207
R-Value Work: 0.163
R-Value Observed: 0.165

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural determination and kinetic analysis of the transketolase from Vibrio vulnificus reveal unexpected cooperative behavior.

Georges, R.N., Ballut, L., Octobre, G., Comte, A., Hecquet, L., Charmantray, F., Doumeche, B.

(2024) Protein Sci 33: e4884-e4884

PubMed: 38145310 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.4884
Primary Citation of Related Structures:
8QMF

PubMed Abstract:
Vibrio vulnificus (vv) is a multidrug-resistant human bacterial pathogen whose prevalence is expected to increase over the years. Transketolases (TK), transferases catalyzing two reactions of the nonoxidative branch of the pentose-phosphate pathway and therefore linked to several crucial metabolic pathways, are potential targets for new drugs against this pathogen. Here, the vvTK is crystallized and its structure is solved at 2.1 Å. A crown of 6 histidyl residues is observed in the active site and expected to participate in the thiamine pyrophosphate (cofactor) activation. Docking of fructose-6-phosphate and ferricyanide used in the activity assay, suggests that both substrates can bind vvTK simultaneously. This is confirmed by steady-state kinetics showing a sequential mechanism, on the contrary to the natural transferase reaction which follows a substituted mechanism. Inhibition by the I38-49 inhibitor (2-(4-ethoxyphenyl)-1-(pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine) reveals for the first time a cooperative behavior of a TK and docking experiments suggest a previously undescribed binding site at the interface between the pyrophosphate and pyridinium domains.

Organizational Affiliation

Univ Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France.

Macromolecule Content

Total Structure Weight: 149.65 kDa
Atom Count: 11,174
Modelled Residue Count: 1,352
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase 2	A, B	678	Vibrio vulnificus YJ016	Mutation(s): 0 Gene Names: tkt2
UniProt
Find proteins for Q7MDD4 (Vibrio vulnificus (strain YJ016)) Explore Q7MDD4 Go to UniProtKB: Q7MDD4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MDD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP (Subject of Investigation/LOI) Query on TPP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain M [auth B]	C [auth A], M [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain D [auth A] SDF format, chain E [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 L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [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 L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions 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 L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density 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 L [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B]	J [auth A], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]