8BZ6 | pdb_00008bz6

Crystal structure of the L. monocytogenes RmlT in complex with UDP-glucose

PDB DOI: https://doi.org/10.2210/pdb8BZ6/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-14 Released: 2023-12-27
Deposition Author(s): Cereija, T.B., Morais-Cabral, J.H.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.195 (Depositor), 0.195 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular properties of the RmlT wall teichoic acid rhamnosyltransferase that modulates virulence in Listeria monocytogenes.

Monteiro, R., Cereija, T.B., Pombinho, R., Voskuilen, T., Codee, J.D.C., Sousa, S., Morais-Cabral, J.H., Cabanes, D.

(2025) Nat Commun 16: 24-24

PubMed: 39746981 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-55360-1
Primary Citation Related Structures:
8BZ4, 8BZ5, 8BZ6, 8BZ7, 8BZ8, 9GZJ, 9GZK

PubMed Abstract:
Wall teichoic acids (WTAs) from the major Gram-positive foodborne pathogen Listeria monocytogenes are peptidoglycan-associated glycopolymers decorated by monosaccharides that, while not essential for bacterial growth, are required for bacterial virulence and resistance to antimicrobials. Here we report the structure and function of a bacterial WTAs rhamnosyltransferase, RmlT, strictly required for L. monocytogenes WTAs rhamnosylation. In particular, we demonstrated that RmlT transfers rhamnose from dTDP-L-rhamnose to naked WTAs, and that specificity towards TDP-rhamnose is not determined by its binding affinity. Structures of RmlT with and without its substrates showed that this enzyme is a dimer, revealed the residues responsible for interaction with the substrates and that the catalytic residue pre-orients the acceptor substrate towards the nucleophilic attack to the sugar. Additionally, the structures provided indications for two potential interaction pathways for the long WTAs on the surface of RmlT. Finally, we confirmed that WTAs glycosyltransferases are promising targets for next-generation strategies against Gram-positive pathogens by showing that inactivation of the RmlT catalytic activity results in a decreased infection in vivo.

Organizational Affiliation

i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. ricardo.monteiro@i3s.up.pt.

Macromolecule Content

Total Structure Weight: 435.39 kDa
Atom Count: 30,490
Modeled Residue Count: 3,635
Deposited Residue Count: 3,744
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B, C, D, E A, B, C, D, E, F	624	Listeria monocytogenes	Mutation(s): 0 Gene Names: APD94_03445 EC: 2.4
UniProt
Find proteins for A0A401AAP7 (Listeria monocytogenes) Explore A0A401AAP7 Go to UniProtKB: A0A401AAP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A401AAP7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UPG (Subject of Investigation/LOI) Query on UPG Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain MA [auth E] SDF format, chain O [auth B] SDF format, chain UA [auth F] SDF format, chain W [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain MA [auth E] MOL2 format, chain O [auth B] MOL2 format, chain UA [auth F] MOL2 format, chain W [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain MA [auth E] mmCIF format, chain O [auth B] mmCIF format, chain UA [auth F] mmCIF format, chain W [auth C]	EA [auth D] G [auth A] MA [auth E] O [auth B] UA [auth F] EA [auth D], G [auth A], MA [auth E], O [auth B], UA [auth F], W [auth C]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-JZMIEXBBSA-N		Interactions Focus chain EA [auth D] Focus chain G [auth A] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain G [auth A] Focus chain MA [auth E] Focus chain O [auth B] Focus chain UA [auth F] Focus chain W [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain FA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain PA [auth E] SDF format, chain Q [auth B] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain U [auth B] SDF format, chain VA [auth F] SDF format, chain X [auth C] SDF format, chain XA [auth F] SDF format, chain YA [auth F] SDF format, chain Z [auth C] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth F] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth F] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth E] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain S [auth B] mmCIF format, chain SA [auth E] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth F] mmCIF format, chain YA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth F]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] FA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], FA [auth D], H [auth A], HA [auth D], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], N [auth A], NA [auth E], PA [auth E], Q [auth B], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth E], T [auth B], TA [auth E], U [auth B], VA [auth F], X [auth C], XA [auth F], YA [auth F], Z [auth C], ZA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain VA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain PA [auth E] Focus chain Q [auth B] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain T [auth B] Focus chain TA [auth E] Focus chain U [auth B] Focus chain VA [auth F] Focus chain X [auth C] Focus chain XA [auth F] Focus chain YA [auth F] Focus chain Z [auth C] Focus chain ZA [auth F]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain V [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain V [auth B] mmCIF format, chain AB [auth F] mmCIF format, chain V [auth B]	AB [auth F], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth F] Focus chain V [auth B] Interactions & Density Focus chain AB [auth F] Focus chain V [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth B] SDF format, chain WA [auth F] SDF format, chain Y [auth C] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain Y [auth C] mmCIF format, chain GA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain P [auth B] mmCIF format, chain WA [auth F] mmCIF format, chain Y [auth C]	GA [auth D] I [auth A] OA [auth E] P [auth B] WA [auth F] GA [auth D], I [auth A], OA [auth E], P [auth B], WA [auth F], Y [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain I [auth A] Focus chain OA [auth E] Focus chain P [auth B] Focus chain WA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth D] Focus chain I [auth A] Focus chain OA [auth E] Focus chain P [auth B] Focus chain WA [auth F] Focus chain Y [auth C]