6CVD | pdb_00006cvd

High resolution crystal structure of FtsY-NG domain of E. coli bound to fragment 1

PDB DOI: https://doi.org/10.2210/pdb6CVD/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-03-27 Released: 2018-08-22
Deposition Author(s): Faoro, C., Ataide, S.F., Kwan, A., Wilkinson-White, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.252 (Depositor), 0.254 (DCC)
R-Value Work:
0.202 (Depositor), 0.206 (DCC)
R-Value Observed:
0.204 (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

Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics.

Faoro, C., Wilkinson-White, L., Kwan, A.H., Ataide, S.F.

(2018) PLoS One 13: e0200387-e0200387

PubMed: 30044812 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0200387
Primary Citation Related Structures:
6CQP, 6CS8, 6CVD, 6DLX

PubMed Abstract:
Given the increasing incidence of antibiotic resistance, antibiotics that employ new strategies are urgently needed. Bacterial survival is dependent on proper function of the signal recognition particle (SRP) and its receptor (FtsY). A unique set of interactions in FtsY:SRP-RNA represents a promising candidate for new antibiotic development as no antibiotic targets this complex and these interactions are functionally replaced by protein:protein interactions in eukaryotes. We used a Fragment Based Drug Design (FBDD) approach to search for new compounds that can bind FtsY, and have identified three lead fragments. In vitro and in vivo analyses have shown that despite a high micromolar binding affinity, one fragment has some antimicrobial properties. X-ray structures of E. coli FtsY:fragments reveal the fragments bind in the targeted RNA interaction site. Our results show that FBDD is a suitable approach for targeting FtsY:SRP-RNA for antibiotic development and opens the possibility of targeting protein:RNA interactions in general.

Organizational Affiliation

School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.

Macromolecule Content

Total Structure Weight: 66.96 kDa
Atom Count: 5,072
Modeled Residue Count: 605
Deposited Residue Count: 606
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle receptor FtsY	A, B	303	Escherichia coli K-12	Mutation(s): 0 Gene Names: ftsY, b3464, JW3429 EC: 3.6.5.4
UniProt
Find proteins for P10121 (Escherichia coli (strain K12)) Explore P10121 Go to UniProtKB: P10121
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4ME Query on 4ME Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	methyl 1H-indole-4-carboxylate C₁₀ H₉ N O₂ WEAXQUBYRSEBJD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]