NRFH_DESVH
ID NRFH_DESVH Reviewed; 159 AA.
AC Q72EF4;
DT 25-APR-2018, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=Cytochrome c nitrite reductase subunit NrfH {ECO:0000303|PubMed:11004582, ECO:0000303|PubMed:16754983};
DE Short=cNiR subunit NrfH {ECO:0000303|PubMed:16754983};
DE AltName: Full=Cytochrome c quinol dehydrogenase NrfH {ECO:0000303|PubMed:17139260};
DE AltName: Full=Cytochrome c-type protein NrfH {ECO:0000305};
GN OrderedLocusNames=DVU_0624 {ECO:0000312|EMBL:AAS95105.1};
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 {ECO:0000312|EMBL:AAS95105.1};
RN [1] {ECO:0000312|EMBL:AAS95105.1, ECO:0000312|Proteomes:UP000002194}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000312|Proteomes:UP000002194};
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 [2]
RP PROTEIN SEQUENCE OF 2-26, FUNCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000303|PubMed:11004582};
RX PubMed=11004582; DOI=10.1016/s0167-4838(00)00111-4;
RA Pereira I.A., LeGall J., Xavier A.V., Teixeira M.;
RT "Characterization of a heme c nitrite reductase from a non-ammonifying
RT microorganism, Desulfovibrio vulgaris Hildenborough.";
RL Biochim. Biophys. Acta 1481:119-130(2000).
RN [3]
RP FUNCTION.
RX PubMed=15547266; DOI=10.1128/jb.186.23.7944-7950.2004;
RA Haveman S.A., Greene E.A., Stilwell C.P., Voordouw J.K., Voordouw G.;
RT "Physiological and gene expression analysis of inhibition of Desulfovibrio
RT vulgaris hildenborough by nitrite.";
RL J. Bacteriol. 186:7944-7950(2004).
RN [4]
RP CRYSTALLIZATION, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000303|PubMed:16754983};
RX PubMed=16754983; DOI=10.1107/s1744309106016629;
RA Rodrigues M.L., Oliveira T., Matias P.M., Martins I.C., Valente F.M.,
RA Pereira I.A., Archer M.;
RT "Crystallization and preliminary structure determination of the membrane-
RT bound complex cytochrome c nitrite reductase from Desulfovibrio vulgaris
RT Hildenborough.";
RL Acta Crystallogr. F 62:565-568(2006).
RN [5]
RP COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, EPR SPECTROSCOPY OF THE NRFHA
RP COMPLEX, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=22519292; DOI=10.1021/jp301356m;
RA Todorovic S., Rodrigues M.L., Matos D., Pereira I.A.;
RT "Redox properties of lysine- and methionine-coordinated hemes ensure
RT downhill electron transfer in NrfH2A4 nitrite reductase.";
RL J. Phys. Chem. B 116:5637-5643(2012).
RN [6]
RP FUNCTION.
RX PubMed=25534748; DOI=10.1021/es504484m;
RA Korte H.L., Saini A., Trotter V.V., Butland G.P., Arkin A.P., Wall J.D.;
RT "Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris
RT Hildenborough and use of nitrite as a substrate for growth.";
RL Environ. Sci. Technol. 49:924-931(2015).
RN [7]
RP INDUCTION.
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000303|PubMed:26283774};
RX PubMed=26283774; DOI=10.1128/jb.00319-15;
RA Rajeev L., Chen A., Kazakov A.E., Luning E.G., Zane G.M., Novichkov P.S.,
RA Wall J.D., Mukhopadhyay A.;
RT "Regulation of Nitrite Stress Response in Desulfovibrio vulgaris
RT Hildenborough, a Model Sulfate-Reducing Bacterium.";
RL J. Bacteriol. 197:3400-3408(2015).
RN [8] {ECO:0007744|PDB:2J7A}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH HEME AND NRFA,
RP FUNCTION, COFACTOR, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000303|PubMed:17139260};
RX PubMed=17139260; DOI=10.1038/sj.emboj.7601439;
RA Rodrigues M.L., Oliveira T.F., Pereira I.A., Archer M.;
RT "X-ray structure of the membrane-bound cytochrome c quinol dehydrogenase
RT NrfH reveals novel haem coordination.";
RL EMBO J. 25:5951-5960(2006).
RN [9] {ECO:0007744|PDB:2VR0}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH HEME; NRFA AND
RP MENAQUINOL ANALOG INHIBITOR, FUNCTION, COFACTOR, SUBUNIT, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
RC {ECO:0000303|PubMed:18597779};
RX PubMed=18597779; DOI=10.1016/j.jmb.2008.05.066;
RA Rodrigues M.L., Scott K.A., Sansom M.S., Pereira I.A., Archer M.;
RT "Quinol oxidation by c-type cytochromes: structural characterization of the
RT menaquinol binding site of NrfHA.";
RL J. Mol. Biol. 381:341-350(2008).
CC -!- FUNCTION: Electron donor subunit of the cytochrome c nitrite reductase
CC holocomplex NrfHA. Acquires electrons from the menaquinone pool and
CC mediates their transfer to the catalytic subunit NrfA in an anaerobic
CC respiratory process of nitrite (PubMed:11004582, PubMed:17139260,
CC PubMed:18597779). The other biological function of the NrfHA
CC holocomplex is to detoxify nitrite (PubMed:15547266, PubMed:25534748).
CC This function is essential for the survival of this organism as it
CC enables it to overcome inhibition by nitrite, which is produced by
CC other organisms living in the same environment (Probable).
CC {ECO:0000269|PubMed:11004582, ECO:0000269|PubMed:15547266,
CC ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779,
CC ECO:0000269|PubMed:25534748, ECO:0000305}.
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779,
CC ECO:0000269|PubMed:22519292};
CC Note=Binds 4 heme groups per subunit. {ECO:0000269|PubMed:17139260};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Redox potential:
CC E(0) is -270 mV for the menaquinol-interacting methionine-coordinated
CC heme 1, identified by the use of the inhibitor 2-heptyl-4-
CC hydroxyquinoline N-oxide (HQNO), a structural analog of the
CC physiological electron donor. {ECO:0000269|PubMed:22519292};
CC -!- SUBUNIT: Component of the NrfHA cytochrome c nitrite reductase complex
CC composed of 4 NrfA catalytic subunits and 2 NrfH quinone-binding
CC subunits (PubMed:17139260, PubMed:18597779, PubMed:22519292). Interacts
CC with NrfA homodimer (PubMed:16754983, PubMed:17139260).
CC {ECO:0000269|PubMed:16754983, ECO:0000269|PubMed:17139260,
CC ECO:0000269|PubMed:18597779, ECO:0000269|PubMed:22519292}.
CC -!- SUBCELLULAR LOCATION: Cell inner membrane {ECO:0000269|PubMed:11004582,
CC ECO:0000269|PubMed:16754983, ECO:0000269|PubMed:17139260,
CC ECO:0000269|PubMed:18597779, ECO:0000269|PubMed:22519292}; Single-pass
CC type II membrane protein {ECO:0000269|PubMed:16754983,
CC ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779}.
CC -!- INDUCTION: Expression is induced by NrfR in response to nitrite stress.
CC Not induced by nitrate or nitric oxide (NO) stress.
CC {ECO:0000269|PubMed:26283774}.
CC -!- SIMILARITY: Belongs to the NapC/NirT/NrfH family. {ECO:0000305}.
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DR EMBL; AE017285; AAS95105.1; -; Genomic_DNA.
DR RefSeq; WP_010937927.1; NZ_CABHLV010000001.1.
DR RefSeq; YP_009846.1; NC_002937.3.
DR PDB; 2J7A; X-ray; 2.30 A; C/F/I/L/O/R=1-159.
DR PDB; 2VR0; X-ray; 2.80 A; C/F=1-159.
DR PDBsum; 2J7A; -.
DR PDBsum; 2VR0; -.
DR AlphaFoldDB; Q72EF4; -.
DR SMR; Q72EF4; -.
DR STRING; 882.DVU_0624; -.
DR DrugBank; DB07918; 2-heptyl-4-hydroxyquinoline N-oxide.
DR PaxDb; Q72EF4; -.
DR EnsemblBacteria; AAS95105; AAS95105; DVU_0624.
DR KEGG; dvu:DVU_0624; -.
DR PATRIC; fig|882.5.peg.582; -.
DR eggNOG; COG3005; Bacteria.
DR HOGENOM; CLU_096753_0_0_7; -.
DR OMA; HYVWKSI; -.
DR PhylomeDB; Q72EF4; -.
DR EvolutionaryTrace; Q72EF4; -.
DR Proteomes; UP000002194; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0019333; P:denitrification pathway; IEA:InterPro.
DR Gene3D; 1.10.3820.10; -; 1.
DR InterPro; IPR029467; Cyt_c7-like.
DR InterPro; IPR036280; Multihaem_cyt_sf.
DR InterPro; IPR024717; NapC/NirT/NrfH.
DR InterPro; IPR005126; NapC/NirT_cyt_c_N.
DR InterPro; IPR038266; NapC/NirT_cytc_sf.
DR Pfam; PF03264; Cytochrom_NNT; 1.
DR Pfam; PF14522; Cytochrome_C7; 1.
DR PIRSF; PIRSF000013; 4_hem_cytochrm_NapC; 1.
DR SUPFAM; SSF48695; SSF48695; 1.
DR PROSITE; PS51008; MULTIHEME_CYTC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane;
KW Direct protein sequencing; Electron transport; Heme; Iron; Membrane;
KW Metal-binding; Reference proteome; Signal-anchor; Stress response;
KW Transmembrane; Transmembrane helix; Transport.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000305|PubMed:11004582"
FT CHAIN 2..159
FT /note="Cytochrome c nitrite reductase subunit NrfH"
FT /evidence="ECO:0000305|PubMed:11004582"
FT /id="PRO_0000444028"
FT TOPO_DOM 2..14
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779"
FT TRANSMEM 15..33
FT /note="Helical; Signal-anchor for type II membrane protein"
FT /evidence="ECO:0000255, ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779"
FT TOPO_DOM 34..159
FT /note="Periplasmic"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779"
FT REGION 99..100
FT /note="Interaction with NrfA"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT REGION 123..158
FT /note="Interaction with NrfA"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 43
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 46
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 49
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 61
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 66
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 67
FT /ligand="a menaquinol"
FT /ligand_id="ChEBI:CHEBI:18151"
FT /evidence="ECO:0000269|PubMed:18597779,
FT ECO:0007744|PDB:2VR0"
FT BINDING 69
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 70
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 82
FT /ligand="a menaquinol"
FT /ligand_id="ChEBI:CHEBI:18151"
FT /evidence="ECO:0000269|PubMed:18597779,
FT ECO:0007744|PDB:2VR0"
FT BINDING 89
FT /ligand="a menaquinol"
FT /ligand_id="ChEBI:CHEBI:18151"
FT /evidence="ECO:0000269|PubMed:18597779,
FT ECO:0007744|PDB:2VR0"
FT BINDING 89
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 116
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 119
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 120
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 136
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="4"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 139
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="4"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT BINDING 140
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="4"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT BINDING 145
FT /ligand="heme"
FT /ligand_id="ChEBI:CHEBI:30413"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A,
FT ECO:0007744|PDB:2VR0"
FT SITE 40
FT /note="Interaction with NrfA"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT SITE 57
FT /note="Interaction with NrfA"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT SITE 63
FT /note="Interaction with NrfA"
FT /evidence="ECO:0000269|PubMed:17139260,
FT ECO:0007744|PDB:2J7A"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 20..36
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 40..43
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 50..58
FT /evidence="ECO:0007829|PDB:2J7A"
FT TURN 60..63
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 75..94
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 106..124
FT /evidence="ECO:0007829|PDB:2J7A"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:2J7A"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 141..143
FT /evidence="ECO:0007829|PDB:2J7A"
FT TURN 144..148
FT /evidence="ECO:0007829|PDB:2J7A"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:2J7A"
SQ SEQUENCE 159 AA; 17263 MW; 0D44379C53D61416 CRC64;
MSEEKSRNGP ARLKLVLGGA TLGVVALATV AFGMKYTDQR PFCTSCHIMN PVGVTHKLSG
HANISCNDCH APHNLLAKLP FKAIAGARDV YMNTLGHPGD LILAGMETKE VVNANCKACH
TMTNVEVASM EAKKYCTDCH RNVQHMRMKP ISTREVADE
