Structure of a [2Fe-2S] Ferredoxin from Rhodobacter Capsulatus Likely Involved in Fe-S Cluster Biogenesis and Conformational Changes Observed Upon Reduction

Overview

Journal J Biol Inorg Chem

Publisher Springer

Specialty Biochemistry

Date 2006 Jan 13

PMID 16402206

Citations 12

Authors

Germaine Sainz

Jean Jakoncic

Larry C Sieker

Vivian Stojanoff

Nukri Sanishvili

Marcel Asso

Patrick Bertrand

Jean Armengaud

Yves Jouanneau

Affiliations

Soon will be listed here.

Abstract

FdVI from Rhodobacter capsulatus is structurally related to a group of [2Fe-2S] ferredoxins involved in iron-sulfur cluster biosynthesis. Comparative genomics suggested that FdVI and orthologs found in alpha-Proteobacteria are involved in this process. Here, the crystal structure of FdVI has been determined for both the oxidized and the reduced protein. The [2Fe-2S] cluster lies 6 A below the protein surface in a hydrophobic pocket without access to the solvent. This particular cluster environment might explain why the FdVI midpoint redox potential (-306 mV at pH 8.0) did not show temperature or ionic strength dependence. Besides the four cysteines that bind the cluster, FdVI features an extra cysteine which is located close to the S1 atom of the cluster and is oriented in a position such that its thiol group points towards the solvent. Upon reduction, the general fold of the polypeptide chain was almost unchanged. The [2Fe-2S] cluster underwent a conformational change from a planar to a distorted lozenge. In the vicinity of the cluster, the side chain of Met24 was rotated by 180 degrees , bringing its S atom within hydrogen-bonding distance of the S2 atom of the cluster. The reduced molecule also featured a higher content of bound water molecules, and more extensive hydrogen-bonding networks compared with the oxidized molecule. The unique conformational changes observed in FdVI upon reduction are discussed in the light of structural studies performed on related ferredoxins.

Citing Articles

Crystal Structure of a Thioredoxin-like Ferredoxin Encoded Within a Cobalamin Biosynthetic Operon of Rhodobacter capsulatus.

Shen Y, Cheng W, Wang X, Dai H, Wang M, Liu L Protein J. 2025; .

PMID: 39924633 DOI: 10.1007/s10930-025-10254-z.

The crystal structure of Shethna protein II (FeSII) from Azotobacter vinelandii suggests a domain swap.

Kabasakal B, McFarlane C, Cotton C, Schmidt A, Kung A, Lieber L Acta Crystallogr D Struct Biol. 2024; 80(Pt 8):599-604.

PMID: 38984904 PMC: 11301756. DOI: 10.1107/S2059798324005928.

Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins.

Mao Z, Liou S, Khadka N, Jenney Jr F, Goodin D, Seefeldt L Biochemistry. 2018; 57(6):978-990.

PMID: 29303562 PMC: 6815397. DOI: 10.1021/acs.biochem.7b01159.

Ultrafast Charge-Transfer Dynamics in the Iron-Sulfur Complex of Rhodobacter capsulatus Ferredoxin VI.

Mao Z, Carroll E, Kim P, Cramer S, Larsen D J Phys Chem Lett. 2017; 8(18):4498-4503.

PMID: 28872878 PMC: 7187928. DOI: 10.1021/acs.jpclett.7b02026.

In crystallo optical spectroscopy (icOS) as a complementary tool on the macromolecular crystallography beamlines of the ESRF.

von Stetten D, Giraud T, Carpentier P, Sever F, Terrien M, Dobias F Acta Crystallogr D Biol Crystallogr. 2015; 71(Pt 1):15-26.

PMID: 25615856 PMC: 4304682. DOI: 10.1107/S139900471401517X.

References

Battistuzzi G, DOnofrio M, Borsari M, Sola M, Macedo A, Moura J . Redox thermodynamics of low-potential iron-sulfur proteins. J Biol Inorg Chem. 2000; 5(6):748-60. DOI: 10.1007/s007750000164. View

Morales R, Charon M, Petillot Y, Norager S, Medina M, Frey M . Refined X-ray structures of the oxidized, at 1.3 A, and reduced, at 1.17 A, [2Fe-2S] ferredoxin from the cyanobacterium Anabaena PCC7119 show redox-linked conformational changes. Biochemistry. 2000; 38(48):15764-73. DOI: 10.1021/bi991578s. View

Berg A, Gustafsson J, Ingelman-Sundberg M . Characterization of a cytochrome P-450-dependent steroid hydroxylase system present in Bacillus megaterium. J Biol Chem. 1976; 251(9):2831-8. View

Lange H, Kaut A, Kispal G, Lill R . A mitochondrial ferredoxin is essential for biogenesis of cellular iron-sulfur proteins. Proc Natl Acad Sci U S A. 2000; 97(3):1050-5. PMC: 15518. DOI: 10.1073/pnas.97.3.1050. View

Nicholls A, Sharp K, Honig B . Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991; 11(4):281-96. DOI: 10.1002/prot.340110407. View

Sevrioukova I . Redox-dependent structural reorganization in putidaredoxin, a vertebrate-type [2Fe-2S] ferredoxin from Pseudomonas putida. J Mol Biol. 2005; 347(3):607-21. DOI: 10.1016/j.jmb.2005.01.047. View

Bertrand P, Gayda J . A theoretical interpretation of the variations of some physical parameters within the [2Fe-2S] ferredoxin group. Biochim Biophys Acta. 1979; 579(1):107-21. DOI: 10.1016/0005-2795(79)90091-6. View

Hase T, Mizutani S, Mukohata Y . Expression of Maize Ferredoxin cDNA in Escherichia coli: Comparison of Photosynthetic and Nonphotosynthetic Ferredoxin Isoproteins and their Chimeric Molecule. Plant Physiol. 1991; 97(4):1395-401. PMC: 1081177. DOI: 10.1104/pp.97.4.1395. View

Sevrioukova I, Garcia C, Li H, Bhaskar B, Poulos T . Crystal structure of putidaredoxin, the [2Fe-2S] component of the P450cam monooxygenase system from Pseudomonas putida. J Mol Biol. 2003; 333(2):377-92. DOI: 10.1016/j.jmb.2003.08.028. View

10.

Beilke D, Weiss R, Lohr F, Pristovsek P, Hannemann F, Bernhardt R . A new electron transport mechanism in mitochondrial steroid hydroxylase systems based on structural changes upon the reduction of adrenodoxin. Biochemistry. 2002; 41(25):7969-78. DOI: 10.1021/bi0160361. View

11.

Armengaud J, Meyer C, Jouanneau Y . Recombinant expression of the fdxD gene of Rhodobacter capsulatus and characterization of its product, a [2Fe-2S] ferredoxin. Biochem J. 1994; 300 ( Pt 2):413-8. PMC: 1138178. DOI: 10.1042/bj3000413. View

12.

BALDWIN J, Morris G, Richards W . Electron transport in cytochromes P-450 by covalent switching. Proc Biol Sci. 1991; 245(1312):43-51. DOI: 10.1098/rspb.1991.0086. View

13.

Coghlan V, Vickery L . Site-specific mutations in human ferredoxin that affect binding to ferredoxin reductase and cytochrome P450scc. J Biol Chem. 1991; 266(28):18606-12. View

14.

Bruschi M, Guerlesquin F . Structure, function and evolution of bacterial ferredoxins. FEMS Microbiol Rev. 1988; 4(2):155-75. DOI: 10.1111/j.1574-6968.1988.tb02741.x. View

15.

Bernhardt R . Cytochrome P450: structure, function, and generation of reactive oxygen species. Rev Physiol Biochem Pharmacol. 1996; 127:137-221. DOI: 10.1007/BFb0048267. View

16.

Takahashi Y, Nakamura M . Functional assignment of the ORF2-iscS-iscU-iscA-hscB-hscA-fdx-ORF3 gene cluster involved in the assembly of Fe-S clusters in Escherichia coli. J Biochem. 1999; 126(5):917-26. DOI: 10.1093/oxfordjournals.jbchem.a022535. View

17.

Kakuta Y, Horio T, Takahashi Y, Fukuyama K . Crystal structure of Escherichia coli Fdx, an adrenodoxin-type ferredoxin involved in the assembly of iron-sulfur clusters. Biochemistry. 2001; 40(37):11007-12. DOI: 10.1021/bi010544t. View

18.

Westbrook E, Naday I . Charge-coupled device-based area detectors. Methods Enzymol. 1997; 276:244-68. View

19.

Ta D, Vickery L . Cloning, sequencing, and overexpression of a [2Fe-2S] ferredoxin gene from Escherichia coli. J Biol Chem. 1992; 267(16):11120-5. View

20.

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View