1YV1

Fully reduced state of nigerythrin (all ferrous)

Summary for 1YV1

• Entry DOI: 10.2210/pdb1yv1/pdb
• Related: 1YUX 1YUZ
• Descriptor: Nigerythrin, FE (II) ION (3 entities in total)
• Functional Keywords: rubrerythrin, rubredoxin, hemerythrin, electron transfer, peroxidase, diiron center, oxidoreductase
• Biological source: Desulfovibrio vulgaris subsp. vulgaris
• Cellular location: Cytoplasm (Probable): P30820
• Total number of polymer chains: 2
• Total formula weight: 44616.92

Authors

Iyer, R.B.,Silaghi-Dumitrescu, R.,Kurtz, D.M.,Lanzilotta, W.N. (deposition date: 2005-02-14, release date: 2005-06-21, Last modification date: 2024-02-14)

Primary citation

Iyer, R.B.,Silaghi-Dumitrescu, R.,Kurtz, D.M.,Lanzilotta, W.N.
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

PubMed 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.

PubMed: 15895271
DOI: 10.1007/s00775-005-0650-8

Experimental method

X-RAY DIFFRACTION (1.5 Å)