9GZK | pdb_00009gzk

Crystal structure of the L. monocytogenes RmlT in complex with 4-RboP-(CH2)6NH2

PDB DOI: https://doi.org/10.2210/pdb9GZK/pdb

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

Deposited: 2024-10-04 Released: 2024-12-18
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: 2.52 Å
R-Value Free:
0.232 (Depositor), 0.222 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.200 (Depositor)

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

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: 437.79 kDa
Atom Count: 29,352
Modeled Residue Count: 3,540
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
UniProt
Find proteins for A0A0H3GFS8 (Listeria monocytogenes serotype 1/2a (strain 10403S)) Explore A0A0H3GFS8 Go to UniProtKB: A0A0H3GFS8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3GFS8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IR6 (Subject of Investigation/LOI) Query on A1IR6 Download:Ideal Coordinates CCD File SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A] I [auth B] J [auth B] L [auth C] O [auth D] G [auth A], I [auth B], J [auth B], L [auth C], O [auth D], Q [auth E], T [auth F], U [auth F]	(Ribitol-phosphate)4-(CH2)6-NH2 C₂₆ H₅₉ N O₂₉ P₄ RCKXLZVGBDVNAH-XRRZROOQSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain T [auth F] Focus chain U [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A]	H [auth A] K [auth B] M [auth C] N [auth C] P [auth D] H [auth A], K [auth B], M [auth C], N [auth C], P [auth D], R [auth E], S [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E]