PHFL_DESVH
ID PHFL_DESVH Reviewed; 421 AA.
AC P07598;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1988, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Periplasmic [Fe] hydrogenase large subunit;
DE EC=1.12.7.2;
DE AltName: Full=Fe hydrogenlyase;
GN Name=hydA; OrderedLocusNames=DVU_1769;
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=3888621; DOI=10.1111/j.1432-1033.1985.tb08869.x;
RA Voordouw G., Brenner S.;
RT "Nucleotide sequence of the gene encoding the hydrogenase from
RT Desulfovibrio vulgaris (Hildenborough).";
RL Eur. J. Biochem. 148:515-520(1985).
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 1-35.
RX PubMed=3322275; DOI=10.1016/0006-291x(87)90376-7;
RA Prickril B.C., He S.H., Li C., Menon N.K., Choi E.S., Przybyla A.E.,
RA Dervartanian D.V., Peck H.D. Jr., Fauque G., le Gall J., Teixeira M.,
RA Moura I., Moura J.J.G., Patil D., Huynh B.H.;
RT "Identification of three classes of hydrogenase in the genus,
RT Desulfovibrio.";
RL Biochem. Biophys. Res. Commun. 149:369-377(1987).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-15.
RA van den Berg W.A.M., Stokkermans J.P.W.G., van Dongen W.M.A.M.;
RL Submitted (SEP-1992) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP MOSSBAUER SPECTROSCOPY OF IRON-SULFUR CLUSTERS.
RX PubMed=11456963; DOI=10.1021/ja003176+;
RA Pereira A.S., Tavares P., Moura I., Moura J.J.G., Huynh B.H.;
RT "Mossbauer characterization of the iron-sulfur clusters in Desulfovibrio
RT vulgaris hydrogenase.";
RL J. Am. Chem. Soc. 123:2771-2782(2001).
RN [6] {ECO:0007744|PDB:1HFE}
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH SMALL SUBUNIT;
RP IRON-SULFUR (4FE-4S) CLUSTERS AND A BINUCLEAR IRON CENTER, AND COFACTOR.
RX PubMed=10368269; DOI=10.1016/s0969-2126(99)80005-7;
RA Nicolet Y., Piras C., Legrand P., Hatchikian E.C., Fontecilla-Camps J.-C.;
RT "Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual
RT coordination to an active site Fe binuclear center.";
RL Structure 7:13-23(1999).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS), ABSORPTION SPECTROSCOPY, EPR
RP SPECTROSCOPY, AND FOURIER-TRANSFORM INFRARED SPECTROSCOPY.
RX PubMed=11456758; DOI=10.1021/ja0020963;
RA Nicolet Y., de Lacey A.L., Vernede X., Fernandez V.M., Hatchikian E.C.,
RA Fontecilla-Camps J.-C.;
RT "Crystallographic and FTIR spectroscopic evidence of changes in Fe
RT coordination upon reduction of the active site of the Fe-only hydrogenase
RT from Desulfovibrio desulfuricans.";
RL J. Am. Chem. Soc. 123:1596-1601(2001).
CC -!- FUNCTION: May be involved in hydrogen uptake for the reduction of
CC sulfate to hydrogen sulfide in an electron transport chain. Cytochrome
CC c3 is likely to be the physiological electron carrier for the enzyme.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2 + 2 oxidized [2Fe-2S]-[ferredoxin] = 2 H(+) + 2 reduced
CC [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:17445, Rhea:RHEA-COMP:10000,
CC Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15378, ChEBI:CHEBI:18276,
CC ChEBI:CHEBI:33737, ChEBI:CHEBI:33738; EC=1.12.7.2;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:10368269};
CC Note=Binds 3 [4Fe-4S] clusters per subunit.
CC {ECO:0000269|PubMed:10368269};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:10368269};
CC Note=Contains an active site Fe binuclear center, which is coordinated
CC by Cys-382 and by non-protein ligands. {ECO:0000269|PubMed:10368269};
CC -!- SUBUNIT: Heterodimer of a large and a small subunit.
CC {ECO:0000269|PubMed:10368269}.
CC -!- SUBCELLULAR LOCATION: Periplasm.
CC -!- MISCELLANEOUS: [Fe], [NiFe], and [NiFeSe] hydrogenases appear to
CC represent three distinct enzymes having hydrogenase activity.
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DR EMBL; X02416; CAA26266.1; -; Genomic_DNA.
DR EMBL; AE017285; AAS96246.1; -; Genomic_DNA.
DR EMBL; Z15142; CAA78848.1; -; Genomic_DNA.
DR PIR; A24551; HQDVFL.
DR RefSeq; WP_010939057.1; NC_002937.3.
DR RefSeq; YP_010987.1; NC_002937.3.
DR PDB; 1E08; NMR; -; A=27-397.
DR PDB; 1GX7; NMR; -; A=27-397.
DR PDB; 1HFE; X-ray; 1.60 A; L/M=1-421.
DR PDBsum; 1E08; -.
DR PDBsum; 1GX7; -.
DR PDBsum; 1HFE; -.
DR AlphaFoldDB; P07598; -.
DR SMR; P07598; -.
DR DIP; DIP-6186N; -.
DR IntAct; P07598; 1.
DR STRING; 882.DVU_1769; -.
DR PaxDb; P07598; -.
DR EnsemblBacteria; AAS96246; AAS96246; DVU_1769.
DR KEGG; dvu:DVU_1769; -.
DR PATRIC; fig|882.5.peg.1625; -.
DR eggNOG; COG1145; Bacteria.
DR eggNOG; COG4624; Bacteria.
DR HOGENOM; CLU_018240_2_0_7; -.
DR OMA; EVMNCAG; -.
DR PhylomeDB; P07598; -.
DR EvolutionaryTrace; P07598; -.
DR Proteomes; UP000002194; Chromosome.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0008901; F:ferredoxin hydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR InterPro; IPR017896; 4Fe4S_Fe-S-bd.
DR InterPro; IPR017900; 4Fe4S_Fe_S_CS.
DR InterPro; IPR009016; Fe_hydrogenase.
DR InterPro; IPR004108; Fe_hydrogenase_lsu_C.
DR InterPro; IPR013352; Fe_hydrogenase_subset.
DR Pfam; PF02906; Fe_hyd_lg_C; 1.
DR Pfam; PF00037; Fer4; 2.
DR SUPFAM; SSF53920; SSF53920; 1.
DR TIGRFAMs; TIGR02512; FeFe_hydrog_A; 1.
DR PROSITE; PS00198; 4FE4S_FER_1; 2.
DR PROSITE; PS51379; 4FE4S_FER_2; 2.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Direct protein sequencing; Electron transport; Iron;
KW Iron-sulfur; Metal-binding; Oxidoreductase; Periplasm; Reference proteome;
KW Repeat; Transport.
FT CHAIN 1..421
FT /note="Periplasmic [Fe] hydrogenase large subunit"
FT /id="PRO_0000159239"
FT DOMAIN 26..57
FT /note="4Fe-4S ferredoxin-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT DOMAIN 59..86
FT /note="4Fe-4S ferredoxin-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00711"
FT BINDING 35
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 41
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 45
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 66
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 69
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 72
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 76
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 179
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 234
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 378
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 382
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT BINDING 382
FT /ligand="Fe(2+)"
FT /ligand_id="ChEBI:CHEBI:29033"
FT /evidence="ECO:0000269|PubMed:10368269,
FT ECO:0007744|PDB:1HFE"
FT CONFLICT 35
FT /note="C -> K (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT STRAND 4..6
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:1HFE"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 40..44
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 81..84
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 88..96
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 108..112
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 114..118
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 127..137
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 140..142
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 145..164
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 172..175
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 180..189
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 191..196
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 203..211
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 214..219
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 223..225
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 226..233
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 236..241
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 256..259
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 260..269
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 274..276
FT /evidence="ECO:0007829|PDB:1HFE"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 291..294
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 295..297
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 301..315
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 325..327
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 332..340
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 343..352
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 353..355
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 356..364
FT /evidence="ECO:0007829|PDB:1HFE"
FT STRAND 371..378
FT /evidence="ECO:0007829|PDB:1HFE"
FT HELIX 382..384
FT /evidence="ECO:0007829|PDB:1HFE"
SQ SEQUENCE 421 AA; 45951 MW; 8E70A0775B68AACD CRC64;
MSRTVMERIE YEMHTPDPKA DPDKLHFVQI DEAKCIGCDT CSQYCPTAAI FGEMGEPHSI
PHIEACINCG QCLTHCPENA IYEAQSWVPE VEKKLKDGKV KCIAMPAPAV RYALGDAFGM
PVGSVTTGKM LAALQKLGFA HCWDTEFTAD VTIWEEGSEF VERLTKKSDM PLPQFTSCCP
GWQKYAETYY PELLPHFSTC KSPIGMNGAL AKTYGAERMK YDPKQVYTVS IMPCIAKKYE
GLRPELKSSG MRDIDATLTT RELAYMIKKA GIDFAKLPDG KRDSLMGEST GGATIFGVTG
GVMEAALRFA YEAVTGKKPD SWDFKAVRGL DGIKEATVNV GGTDVKVAVV HGAKRFKQVC
DDVKAGKSPY HFIEYMACPG GCVCGGGQPV MPGVLEAMDR TTTRLYAGLK KRLAMASANK
A
