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High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins

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An Erratum to this article was published on 26 July 2005

Abstract

High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-Å movement of one iron (Fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([Fe2(II),Fe1(III)]) to diferrous states, even at cryogenic temperatures. This Glu↔His ligand “toggling” of one iron, which also occurs in DvRbr, thus, appears to be a characteristic feature of Rbr-type diiron sites. Unique features of DvNgr revealed by these structures include redox-induced flipping of a peptide carbonyl that reversibly forms a hydrogen bond to the histidine ligand to Fe1 of the diiron site, an intra-subunit proximal orientation of the rubredoxin-(Rub)-like and diiron domains, and an electron transfer pathway consisting of six covalent and two hydrogen bonds connecting the Rub-like iron with Fe2 of the diiron site. This pathway can account for DvNgr’s relatively rapid peroxidase turnover. The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen.

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Abbreviations

Rbr:

rubrerythrin

Rub:

rubredoxin

Ngr:

nigerythrin

Dv:

Desulfovibrio vulgaris

ENDOR:

Electron-nuclear double resonance

ZnS4Rbr:

Rbr with zinc in the Rub-like site

PEG:

polyethylene glycol

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Acknowledgements

This work was supported by NIH grant GM40388 (D.M.K.). R.S.D. thanks the Chemistry Department of Babesh-Bolyai University, Cluj-Napoca, Romania, for a leave of absence. The authors would also like to thank B.C. Wang for providing the software ISAS and James Imlay for providing strain JI377.

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Authors and Affiliations

  1. Department of Chemistry, University of Georgia, Athens, GA, 30602, USA

    Ramesh B. Iyer, Radu Silaghi-Dumitrescu & Donald M. Kurtz Jr

  2. Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA

    William N. Lanzilotta

  3. Center for Metalloenzyme Studies, University of Georgia, Athens, GA, 30602, USA

    Ramesh B. Iyer, Radu Silaghi-Dumitrescu, Donald M. Kurtz Jr & William N. Lanzilotta

Authors
  1. Ramesh B. Iyer
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  2. Radu Silaghi-Dumitrescu
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  3. Donald M. Kurtz Jr
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  4. William N. Lanzilotta
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Corresponding author

Correspondence to William N. Lanzilotta.

Additional information

An erratum to this article can be found at http://dx.doi.org/10.1007/s00775-005-0667-z

Ramesh B. Iyer and Radu Silaghi-Dumitrescu contributed equally to this work.

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Iyer, R.B., Silaghi-Dumitrescu, R., Kurtz, D.M. et al. High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins. J Biol Inorg Chem 10, 407–416 (2005). https://doi.org/10.1007/s00775-005-0650-8

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  • DOI: https://doi.org/10.1007/s00775-005-0650-8

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