7YRA | pdb_00007yra

Crystal structure of [2Fe-2S]-TtPetA

PDB DOI: https://doi.org/10.2210/pdb7YRA/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Thermochromatium tepidum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-09 Released: 2023-09-20
Deposition Author(s): Tsutsumi, E., Niwa, S., Takeda, K.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.239 (Depositor), 0.230 (DCC)
R-Value Work:
0.207 (Depositor), 0.204 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride.

Tsutsumi, E., Niwa, S., Takeda, R., Sakamoto, N., Okatsu, K., Fukai, S., Ago, H., Nagao, S., Sekiguchi, H., Takeda, K.

(2023) Commun Chem 6: 190-190

PubMed: 37689761 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42004-023-01000-6
Primary Citation Related Structures:
7YR9, 7YRA

PubMed Abstract:
Iron-sulfur clusters are prosthetic groups of proteins involved in various biological processes. However, details of the immature state of the iron-sulfur cluster into proteins have not yet been elucidated. We report here the first structural analysis of the Zn-containing form of a Rieske-type iron-sulfur protein, PetA, from Thermochromatium tepidum (TtPetA) by X-ray crystallography and small-angle X-ray scattering analysis. The Zn-containing form of TtPetA was indicated to be a dimer in solution. The zinc ion adopts a regular tetra-coordination with two chloride ions and two cysteine residues. Only a histidine residue in the cluster-binding site exhibited a conformational difference from the [2Fe-2S] containing form. The Zn-containing structure indicates that the conformation of the cluster binding site is already constructed and stabilized before insertion of [2Fe-2S]. The binding mode of ZnCl ₂, similar to the [2Fe-2S] cluster, suggests that the zinc ions might be involved in the insertion of the [2Fe-2S] cluster.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 33.95 kDa
Atom Count: 2,465
Modeled Residue Count: 292
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquinol-cytochrome c reductase iron-sulfur subunit	A, B	149	Thermochromatium tepidum	Mutation(s): 0 Gene Names: petA EC: 7.1.1.8
UniProt
Find proteins for D1MZ11 (Thermochromatium tepidum) Explore D1MZ11 Go to UniProtKB: D1MZ11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1MZ11
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	D [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], K [auth B], L [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]