7B5G | pdb_00007b5g

Crystal structure of E.coli LexA in complex with nanobody NbSOS3(Nb14527)

• PDB DOI: https://doi.org/10.2210/pdb7B5G/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12, Lama glama
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-03 Released: 2022-09-14 
• Deposition Author(s): Maso, L., Vascon, F., Chinellato, M., Pardon, E., Steyaert, J., Angelini, A., Tondi, D., Cendron, L.
• Funding Organization(s): Italian Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Nanobodies targeting LexA autocleavage disclose a novel suppression strategy of SOS-response pathway.

Maso, L., Vascon, F., Chinellato, M., Goormaghtigh, F., Bellio, P., Campagnaro, E., Van Melderen, L., Ruzzene, M., Pardon, E., Angelini, A., Celenza, G., Steyaert, J., Tondi, D., Cendron, L.

(2022) Structure 30: 1479

• PubMed: 36240773 
• DOI: https://doi.org/10.1016/j.str.2022.09.004
• Primary Citation Related Structures: 
  7B5G, 7OCJ, 7ZRA


• PubMed Abstract: 
  

  Antimicrobial resistance threatens the eradication of infectious diseases and impairs the efficacy of available therapeutics. The bacterial SOS pathway is a conserved response triggered by genotoxic stresses and represents one of the principal mechanisms that lead to resistance. The RecA recombinase acts as a DNA-damage sensor inducing the autoproteolysis of the transcriptional repressor LexA, thereby derepressing SOS genes that mediate DNA repair, survival to chemotherapy, and hypermutation. The inhibition of such pathway represents a promising strategy for delaying the evolution of antimicrobial resistance. We report the identification, via llama immunization and phage display, of nanobodies that bind LexA with sub-micromolar affinity and block autoproteolysis, repressing SOS response in Escherichia coli. Biophysical characterization of nanobody-LexA complexes revealed that they act by trapping LexA in an inactive conformation and interfering with RecA engagement. Our studies pave the way to the development of new-generation antibiotic adjuvants for the treatment of bacterial infections.

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Organizational Affiliation: 
• Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
Biozentrum, University of Basel, CH-4056 Basel, Switzerland; Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), 12 rue des Professeurs Jeener et Brachet, B-6041 Brussels, Belgium.
Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell'Aquila, Via Vetoio 1, 67100 L'Aquila, Italy.
Cellular and Molecular Microbiology (CM2), Faculté des Sciences, Université Libre de Bruxelles (ULB), 12 rue des Professeurs Jeener et Brachet, B-6041 Brussels, Belgium.
Dipartimento di Scienze Biomediche, Università degli Studi di Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy.
VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari Venezia, via Torino 155, 30172 Mestre, Venice, Italy.
Dipartimento di Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via Giuseppe Campi 103, 41125 Modena, Italy.
Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 147.13 kDa 
• Atom Count: 7,961 
• Modeled Residue Count: 1,017 
• Deposited Residue Count: 1,336 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LexA repressor	A, C, E, G	202	Escherichia coli K-12	Mutation(s): 0  Gene Names: lexA, exrA, spr, tsl, umuA, b4043, JW4003 EC: 3.4.21.88
UniProt
Find proteins for P0A7C2 (Escherichia coli (strain K12)) Explore P0A7C2  Go to UniProtKB:  P0A7C2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb14527, NbSOS3	B, D, F, H	132	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	I [auth A], J [auth A], K [auth C], L [auth C], M [auth C], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.252 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.067	α = 84.53
b = 57.081	β = 83.21
c = 122.506	γ = 68.43

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Maso, L., Vascon, F., Chinellato, M., Pardon, E., Steyaert, J., Angelini, A., Tondi, D., Cendron, L.

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Funding Organization	Location	Grant Number
Italian Ministry of Education	Italy	--

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 1.2: 2022-11-16
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary