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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.

Iyer RB, Silaghi-Dumitrescu R, Kurtz DM, Lanzilotta WN
J Biol Inorg Chem 10 407-16 (2005)
Related entries: 1yux, 1yuz

Cited: 22 times
EuropePMC logo PMID: 15895271

Abstract

High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-A 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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  3. RbrA, a cyanobacterial rubrerythrin, functions as a FNR-dependent peroxidase in heterocysts in protection of nitrogenase from damage by hydrogen peroxide in Anabaena sp. PCC 7120. Zhao W, Ye Z, Zhao J. Mol Microbiol 66 1219-1230 (2007)
  4. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. J Mol Biol 388 356-380 (2009)
  5. Aerobic Lineage of the Oxidative Stress Response Protein Rubrerythrin Emerged in an Ancient Microaerobic, (Hyper)Thermophilic Environment. Cardenas JP, Quatrini R, Holmes DS. Front Microbiol 7 1822 (2016)
  6. A Photosynthesis-Specific Rubredoxin-Like Protein Is Required for Efficient Association of the D1 and D2 Proteins during the Initial Steps of Photosystem II Assembly. Kiss É, Knoppová J, Aznar GP, Pilný J, Yu J, Halada P, Nixon PJ, Sobotka R, Komenda J. Plant Cell 31 2241-2258 (2019)
  7. Histidine ligand variants of a flavo-diiron protein: effects on structure and activities. Fang H, Caranto JD, Mendoza R, Taylor AB, Hart PJ, Kurtz DM. J Biol Inorg Chem 17 1231-1239 (2012)
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  13. Redox and acid-base properties of asymmetric non-heme (hydr)oxo-bridged diiron complexes. Jozwiuk A, Ingram AL, Powell DR, Moubaraki B, Chilton NF, Murray KS, Houser RP. Dalton Trans 43 9740-9753 (2014)
  14. Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily. Cooley RB, Arp DJ, Karplus PA. J Mol Biol 413 177-194 (2011)


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