8R3S | pdb_00008r3s

Transketolase from Staphylococcus aureus in complex with thiamin pyrophosphate

PDB DOI: https://doi.org/10.2210/pdb8R3S/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-10 Released: 2024-05-22
Deposition Author(s): Ballut, L., Georges, N., Aghajari, N., Hecquet, L., Charmantray, F., Doumeche, B.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.260 (Depositor), 0.261 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: in silico
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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

Biochemical, Bioinformatic, and Structural Comparisons of Transketolases and Position of Human Transketolase in the Enzyme Evolution.

Georges, R.N., Ballut, L., Aghajari, N., Hecquet, L., Charmantray, F., Doumeche, B.

(2024) Biochemistry 63: 1460-1473

PubMed: 38767928 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.3c00714
Primary Citation Related Structures:
8R3O, 8R3P, 8R3Q, 8R3R, 8R3S

PubMed Abstract:
Transketolases (TKs) are key enzymes of the pentose phosphate pathway, regulating several other critical pathways in cells. Considering their metabolic importance, TKs are expected to be conserved throughout evolution. However, Tittmann et al. ( J Biol Chem , 2010 , 285(41): 31559-31570) demonstrated that Homo sapiens TK ( hs TK) possesses several structural and kinetic differences compared to bacterial TKs. Here, we study 14 TKs from pathogenic bacteria, fungi, and parasites and compare them with hs TK using biochemical, bioinformatic, and structural approaches. For this purpose, six new TK structures are solved by X-ray crystallography, including the TK of Plasmodium falciparum . All of these TKs have the same general fold as bacterial TKs. This comparative study shows that hs TK greatly differs from TKs from pathogens in terms of enzymatic activity, spatial positions of the active site, and monomer-monomer interface residues. An ubiquitous structural pattern is identified in all TKs as a six-residue histidyl crown around the TK cofactor (thiamine pyrophosphate), except for hs TK containing only five residues in the crown. Residue mapping of the monomer-monomer interface and the active site reveals that hs TK contains more unique residues than other TKs. From an evolutionary standpoint, TKs from animals (including H. sapiens ) and Schistosoma sp. belong to a distinct structural group from TKs of bacteria, plants, fungi, and parasites, mostly based on a different linker between domains, raising hypotheses regarding evolution and regulation.

Organizational Affiliation

Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ICBMS UMR5246, 69622 Villeurbanne, France.

Macromolecule Content

Total Structure Weight: 746.99 kDa
Atom Count: 51,300
Modeled Residue Count: 6,624
Deposited Residue Count: 6,770
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transketolase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	677	Staphylococcus aureus	Mutation(s): 0 Gene Names: tkt, SA1177 EC: 2.2.1.1
UniProt
Find proteins for P99161 (Staphylococcus aureus (strain N315)) Explore P99161 Go to UniProtKB: P99161
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P99161
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] SDF format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain P [auth C] SDF format, chain DA [auth J] MOL2 format, chain BA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain P [auth C] MOL2 format, chain DA [auth J] mmCIF format, chain BA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain P [auth C] mmCIF format, chain DA [auth J]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]