8S7G | pdb_00008s7g

Cryo-EM structure of Pseudomonas aeruginosa Recombinase A (RecA) in complex with LexAS125A mutant

PDB DOI: https://doi.org/10.2210/pdb8S7G/pdb
EM Map EMD-19771: EMDB EMDataResource
NAKB: 8S7G

Classification: TRANSCRIPTION
Organism(s): Pseudomonas aeruginosa, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-03-01 Released: 2025-01-15
Deposition Author(s): De Felice, S., Vascon, F., Huber, S.T., Catalano, C., Jakobi, A.J., Cendron, L.
Funding Organization(s): Italian Ministry of Education

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.43 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Snapshots of Pseudomonas aeruginosa SOS response reveal structural requisites for LexA autoproteolysis.

Vascon, F., De Felice, S., Gasparotto, M., Huber, S.T., Catalano, C., Chinellato, M., Mezzetti, R., Grinzato, A., Filippini, F., Maso, L., Jakobi, A.J., Cendron, L.

(2025) iScience 28: 111726-111726

PubMed: 39898034 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.isci.2024.111726
Primary Citation Related Structures:
8B0V, 8S70, 8S7G

PubMed Abstract:
Antimicrobial resistance poses a severe threat to human health and Pseudomonas aeruginosa stands out among the pathogens responsible for this emergency. The SOS response to DNA damage is crucial in bacterial evolution, influencing resistance development and adaptability in challenging environments, especially under antibiotic exposure. Recombinase A (RecA) and the transcriptional repressor LexA are the key players that orchestrate this process, determining either the silencing or the active transcription of the genes under their control. By integrating state-of-the-art structural approaches with in vitro binding and functional assays, we elucidated the molecular events activating the SOS response in P. aeruginosa , focusing on the RecA-LexA interaction. Our findings identify the conserved determinants and strength of the interactions that allow RecA to trigger LexA autocleavage and inactivation. These results provide the groundwork for designing novel antimicrobial strategies and exploring the potential translation of Escherichia coli -derived approaches, to address the implications of P. aeruginosa infections.

Organizational Affiliation

Department of Biology, University of Padua, Via Ugo Bassi 58/b, 35131 Padova, Italy.

Macromolecule Content

Total Structure Weight: 491.04 kDa
Atom Count: 30,036
Modeled Residue Count: 3,892
Deposited Residue Count: 4,429
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LexA repressor	A, B	211	Pseudomonas aeruginosa	Mutation(s): 1 Gene Names: lexA, PA3007 EC: 3.4.21.88
UniProt
Find proteins for P37452 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P37452 Go to UniProtKB: P37452
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P37452
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein RecA	C [auth D] D [auth E] E [auth F] F [auth G] G [auth H] C [auth D], D [auth E], E [auth F], F [auth G], G [auth H], H [auth I], I [auth J], J [auth K], K [auth L], M [auth C], N [auth M]	361	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: recA, PA3617
UniProt
Find proteins for P08280 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P08280 Go to UniProtKB: P08280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08280
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (36-MER)	L [auth T]	36	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain JA [auth M] SDF format, chain HA [auth C] SDF format, chain FA [auth L] SDF format, chain DA [auth K] SDF format, chain BA [auth J] MOL2 format, chain Z [auth I] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain JA [auth M] MOL2 format, chain HA [auth C] MOL2 format, chain FA [auth L] MOL2 format, chain DA [auth K] MOL2 format, chain BA [auth J] mmCIF format, chain Z [auth I] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain JA [auth M] mmCIF format, chain HA [auth C] mmCIF format, chain FA [auth L] mmCIF format, chain DA [auth K] mmCIF format, chain BA [auth J]	BA [auth J] DA [auth K] FA [auth L] HA [auth C] JA [auth M] BA [auth J], DA [auth K], FA [auth L], HA [auth C], JA [auth M], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H], Z [auth I]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain BA [auth J] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain HA [auth C] Focus chain JA [auth M] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I] Interactions & Density Focus chain BA [auth J] Focus chain DA [auth K] Focus chain FA [auth L] Focus chain HA [auth C] Focus chain JA [auth M] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth I] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain IA [auth M] SDF format, chain GA [auth C] SDF format, chain EA [auth L] SDF format, chain CA [auth K] SDF format, chain AA [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain IA [auth M] MOL2 format, chain GA [auth C] MOL2 format, chain EA [auth L] MOL2 format, chain CA [auth K] MOL2 format, chain AA [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain IA [auth M] mmCIF format, chain GA [auth C] mmCIF format, chain EA [auth L] mmCIF format, chain CA [auth K] mmCIF format, chain AA [auth J]	AA [auth J] CA [auth K] EA [auth L] GA [auth C] IA [auth M] AA [auth J], CA [auth K], EA [auth L], GA [auth C], IA [auth M], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H], Y [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain CA [auth K] Focus chain EA [auth L] Focus chain GA [auth C] Focus chain IA [auth M] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I] Interactions & Density Focus chain AA [auth J] Focus chain CA [auth K] Focus chain EA [auth L] Focus chain GA [auth C] Focus chain IA [auth M] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Focus chain Y [auth I]