8Y30 | pdb_00008y30

Crystal structure of Staphylococcus aureus RecJ protein in complex with Mg2+

PDB DOI: https://doi.org/10.2210/pdb8Y30/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-01-27 Released: 2025-01-29
Deposition Author(s): Cheng, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.246 (Depositor), 0.245 (DCC)
R-Value Observed:
0.247 (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

Structural and functional characterization of Staphylococcus aureus RecJ reveals CTD-mediated functional divergence in DNA repair mechanisms.

Gao, J., Sun, Y., Xu, X., Wang, Y., Wang, Y., Shi, T., Wu, S., Cheng, K.

(2026) Protein Sci 35: e70484-e70484

PubMed: 41556491 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70484
Primary Citation Related Structures:
8Y30

PubMed Abstract:
Staphylococcus aureus is a major human pathogen that tolerates diverse environmental stresses, and multidrug-resistant strains pose serious clinical challenges. RecJ, a nuclease involved in DNA repair, contributes to stress resistance, yet its structural and mechanistic features in S. aureus remain unclear. Here, we classified bacterial RecJ proteins into six subtypes based on the geometry of their C-terminal domains (CTDs) and performed structural and biochemical characterization of S. aureus RecJ (SaRecJ, SA-type) in comparison with Deinococcus radiodurans RecJ (DrRecJ, DR-type). Biochemical assays revealed that SaRecJ is a Mg ²⁺-dependent 5'-3' exonuclease that remains active under high-temperature and high-salt conditions, consistent with the stress-tolerant physiology of S. aureus. The 2.8 Å crystal structure of SaRecJ revealed distinctive CTD conformations and the absence of the canonical SSB-binding pocket observed in DrRecJ. Functional analyses further suggested that the CTD contributes to SaRecJ stability and long ssDNA resection. Unlike DrRecJ, SaRecJ specifically participates in the repair of mitomycin C (MMC)-induced DNA cross-links. Moreover, SaRecJ cooperates with the helicase-nuclease SaDinG for coordinated DNA end resection. Collectively, these results define a CTD-driven functional specialization of RecJ and reveal how S. aureus remodels its DNA repair machinery to maintain genome integrity under cross-linking stress.

Organizational Affiliation

Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou, China.

Macromolecule Content

Total Structure Weight: 258.14 kDa
Atom Count: 18,142
Modeled Residue Count: 2,268
Deposited Residue Count: 2,271
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded-DNA-specific exonuclease RecJ	A, B, C	757	Staphylococcus aureus	Mutation(s): 0 Gene Names: recJ, C7M54_09320, DD547_01719, EP54_09380, EQ90_02295, FAF17_07585, GO736_02485, GO814_13090, GO942_04975, GQX37_04600... recJ, C7M54_09320, DD547_01719, EP54_09380, EQ90_02295, FAF17_07585, GO736_02485, GO814_13090, GO942_04975, GQX37_04600, HMPREF3211_01788, NCTC10702_02567, NCTC13131_01854, SAHC1335_02661, SAMEA103891415_01718, SAMEA2076235_02465, SAMEA2078260_02401, SAMEA2078588_02434, SAMEA2078837_02538, SAMEA2080344_02433, SAMEA2081063_02523, SAMEA4008575_02672
UniProt
Find proteins for Q2FXT9 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXT9 Go to UniProtKB: Q2FXT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2FXT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	D [auth A] E [auth A] I [auth B] J [auth B] N [auth C] D [auth A], E [auth A], I [auth B], J [auth B], N [auth C], O [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C]