NIGY_DESVH
ID NIGY_DESVH Reviewed; 202 AA.
AC P30820;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2004, sequence version 3.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Nigerythrin;
GN Name=ngr; OrderedLocusNames=DVU_0019;
OS Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM
OS B-1760 / Hildenborough).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=882;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9226272; DOI=10.1128/jb.179.14.4607-4615.1997;
RA Lumppio H.L., Shenvi N.V., Garg R.P., Summers A.O., Kurtz D.M. Jr.;
RT "A rubrerythrin operon and nigerythrin gene in Desulfovibrio vulgaris
RT (Hildenborough).";
RL J. Bacteriol. 179:4607-4615(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough;
RX PubMed=15077118; DOI=10.1038/nbt959;
RA Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T.,
RA Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M.,
RA Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R.,
RA Nelson W.C., Sullivan S.A., Fouts D.E., Haft D.H., Selengut J.,
RA Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G.,
RA Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V.,
RA Wall J.D., Voordouw G., Fraser C.M.;
RT "The genome sequence of the anaerobic, sulfate-reducing bacterium
RT Desulfovibrio vulgaris Hildenborough.";
RL Nat. Biotechnol. 22:554-559(2004).
RN [3]
RP PROTEIN SEQUENCE OF 1-15.
RX PubMed=8383040; DOI=10.1111/j.1432-1033.1993.tb17655.x;
RA Pierik A.J., Wolbert R.B.G., Portier G.L., Verhagen M.F.J.M., Hagen W.R.;
RT "Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two
RT mononuclear iron centers and two dinuclear iron clusters.";
RL Eur. J. Biochem. 212:237-245(1993).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), AND IRON-BINDING SITES.
RX PubMed=15895271; DOI=10.1007/s00775-005-0650-8;
RA Iyer R.B., Silaghi-Dumitrescu R., Kurtz D.M. Jr., Lanzilotta W.N.;
RT "High-resolution crystal structures of Desulfovibrio vulgaris
RT (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain
RT interface variability, and peroxidase activity in the rubrerythrins.";
RL J. Biol. Inorg. Chem. 10:407-416(2005).
CC -!- FUNCTION: Exhibits NADH peroxidase activity (in vitro).
CC -!- SUBUNIT: Homodimer. May possess two rubredoxin-like centers and two
CC hemerythrin-like binuclear-iron centers per dimer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
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DR EMBL; U71215; AAC45480.1; -; Genomic_DNA.
DR EMBL; AE017285; AAS94503.1; -; Genomic_DNA.
DR RefSeq; WP_010937330.1; NZ_CABHLV010000001.1.
DR RefSeq; YP_009244.1; NC_002937.3.
DR PDB; 1YUX; X-ray; 1.60 A; A/B=1-202.
DR PDB; 1YUZ; X-ray; 1.40 A; A/B=1-202.
DR PDB; 1YV1; X-ray; 1.50 A; A/B=1-202.
DR PDBsum; 1YUX; -.
DR PDBsum; 1YUZ; -.
DR PDBsum; 1YV1; -.
DR AlphaFoldDB; P30820; -.
DR SMR; P30820; -.
DR IntAct; P30820; 1.
DR PaxDb; P30820; -.
DR EnsemblBacteria; AAS94503; AAS94503; DVU_0019.
DR KEGG; dvu:DVU_0019; -.
DR PATRIC; fig|882.5.peg.16; -.
DR eggNOG; COG1592; Bacteria.
DR HOGENOM; CLU_095256_1_0_7; -.
DR OMA; NEVHICS; -.
DR PhylomeDB; P30820; -.
DR EvolutionaryTrace; P30820; -.
DR Proteomes; UP000002194; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:InterPro.
DR CDD; cd01041; Rubrerythrin; 1.
DR Gene3D; 1.20.1260.10; -; 1.
DR InterPro; IPR012347; Ferritin-like.
DR InterPro; IPR009040; Ferritin-like_diiron.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR024934; Rubredoxin-like_dom.
DR InterPro; IPR003251; Rubrerythrin.
DR Pfam; PF02915; Rubrerythrin; 1.
DR SUPFAM; SSF47240; SSF47240; 1.
DR PROSITE; PS50905; FERRITIN_LIKE; 1.
DR PROSITE; PS50903; RUBREDOXIN_LIKE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Electron transport;
KW Iron; Metal-binding; Reference proteome; Transport.
FT CHAIN 1..202
FT /note="Nigerythrin"
FT /id="PRO_0000135072"
FT DOMAIN 23..168
FT /note="Ferritin-like diiron"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00085"
FT DOMAIN 169..202
FT /note="Rubredoxin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00241"
FT BINDING 40
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 73
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 73
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 115
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 118
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 149
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT BINDING 149
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 152
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT BINDING 174
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="3"
FT BINDING 177
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="3"
FT BINDING 189
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="3"
FT BINDING 192
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="3"
FT CONFLICT 129
FT /note="K -> E (in Ref. 1; AAC45480)"
FT /evidence="ECO:0000305"
FT CONFLICT 132
FT /note="E -> G (in Ref. 1; AAC45480)"
FT /evidence="ECO:0000305"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 29..56
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 60..87
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 104..120
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 122..133
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 136..161
FT /evidence="ECO:0007829|PDB:1YUZ"
FT TURN 162..164
FT /evidence="ECO:0007829|PDB:1YUZ"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1YUZ"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:1YUZ"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:1YUZ"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:1YUZ"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:1YUZ"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:1YUZ"
SQ SEQUENCE 202 AA; 22098 MW; DF5410519EE8D899 CRC64;
MKVRAQVPTV KNATNFNMVA DSKTAVGSTL ENLKAAIAGE TGAHAKYTAF AKAAREQGYE
QIARLFEATA AAELIHIGLE YALVAEMEPG YEKPTVAAPS AYSCDLNLIS GANGEIYETS
DMYPAFIRKA QEEGNSKAVH VFTRAKLAES VHAERYLAAY NDIDAPDDDK FHLCPICGYI
HKGEDFEKCP ICFRPKDTFT AY
