9R7J | pdb_00009r7j

Repair of Iron Centre (RIC) protein from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb9R7J/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-14 Released: 2025-07-09
Deposition Author(s): Romao, C.V., Matias, P.M., Saraiva, L.M.
Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.296 (Depositor), 0.293 (DCC)
R-Value Work:
0.263 (Depositor), 0.261 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Interaction of Staphylococcus aureus di-iron Repair of Iron Centers protein with the iron-sulfur cluster assembly SUF system.

Lourenco, F.M., Silva, L.S.O., Almeida, M.R., Folgosa, F., Matias, P.M., Carvalho, S.M., Lima, J.C., Romao, C.V., Saraiva, L.M.

(2026) Protein Sci 35: e70406-e70406

PubMed: 41427678 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.70406
Primary Citation of Related Structures:
9R7J

PubMed Abstract:
Repair of Iron Centers (RIC) proteins are present in several pathogens, including Staphylococcus aureus, contributing to resistance to nitroxidative stress and virulence. In this work, we investigated the molecular mechanisms by which S. aureus RIC facilitates iron mobilization, through structural analyses and functional studies. EPR spectroscopy shows that S. aureus RIC contains an antiferromagnetically coupled di-iron site, undergoing two sequential monoelectronic transitions with a reduction potential of +185 mV. The protein exhibits a stronger affinity for Fe ³⁺ and releases Fe ²⁺ more readily, suggesting facilitated Fe ²⁺ mobilization. The first crystallographic structure for this protein reveals that the di-iron center is embedded in a four-helix bundle domain and is coordinated by histidine residues (H87, H211, H132, H167) and bidentate glutamates (E136, E215). Additionally, we observed that RIC contains one protein tunnel formed by M129 and T170 residues, which are shown to facilitate iron release. In S. aureus, the operon encoding Fe-S biogenesis SUF (SUlFur mobilization) system contains a cysteine desulfurase SufS, a persulfide transporter SufU, and a putative Fe-S scaffold complex SufBC₂D similar to that of Escherichia coli. We show that RIC promotes the assembly of a Fe-S cluster in E. coli SufBC₂D. In S. aureus, we observed the interactions between SufU-SufD and SufC-SufD, which provide the first evidence for the actual formation of this scaffold in the pathogen. Notably, RIC directly interacts with central components of the Fe-S cluster biogenesis, specifically SufS, SufU, and SufD.

Organizational Affiliation

Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.

Macromolecule Content

Total Structure Weight: 102.84 kDa
Atom Count: 5,235
Modeled Residue Count: 633
Deposited Residue Count: 896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur cluster repair protein ScdA	A, B, C, D	224	Staphylococcus aureus	Mutation(s): 0 Gene Names: scdA, SAUSA300_0253
UniProt
Find proteins for P72360 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P72360 Go to UniProtKB: P72360
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P72360
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A]	H [auth A], L [auth B], P [auth C], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]
FE (Subject of Investigation/LOI) Query on FE Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] M [auth C] E [auth A], F [auth A], I [auth B], J [auth B], M [auth C], N [auth C], R [auth D], S [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain R [auth D] Focus chain S [auth D]
O (Subject of Investigation/LOI) Query on O Download Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B], O [auth C], T [auth D]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]