PHNS_SOLFR
ID PHNS_SOLFR Reviewed; 314 AA.
AC P18187;
DT 01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
DT 22-JUL-2008, sequence version 4.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Periplasmic [NiFe] hydrogenase small subunit;
DE EC=1.12.2.1;
DE AltName: Full=NiFe hydrogenlyase small chain;
DE Flags: Precursor;
GN Name=hydA;
OS Solidesulfovibrio fructosivorans (Desulfovibrio fructosivorans).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Solidesulfovibrio.
OX NCBI_TaxID=878;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 49200 / DSM 3604 / VKM B-1801 / JJ;
RX PubMed=2227457; DOI=10.1016/0378-1119(90)90473-5;
RA Rousset M., Dermoun Z., Matchikian C.E., Belaich J.-P.;
RT "Cloning and sequencing of the locus encoding the large and small subunit
RT genes of the periplasmic [NiFe]hydrogenase from Desulfovibrio
RT fructosovorans.";
RL Gene 94:95-101(1990).
RN [2]
RP PROTEIN SEQUENCE OF 50-60.
RX PubMed=2154378; DOI=10.1111/j.1432-1033.1990.tb15347.x;
RA Hatchikian C.E., Traore A.S., Fernandez V.M., Cammack R.;
RT "Characterization of the nickel-iron periplasmic hydrogenase from
RT Desulfovibrio fructosovorans.";
RL Eur. J. Biochem. 187:635-643(1990).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 51-314 IN COMPLEX WITH HYDB AND
RP IRON-SULFUR CLUSTERS, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF
RP PRO-238.
RX PubMed=9751716; DOI=10.1073/pnas.95.20.11625;
RA Rousset M., Montet Y., Guigliarelli B., Forget N., Asso M., Bertrand P.,
RA Fontecilla-Camps J.C., Hatchikian E.C.;
RT "[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans
RT [NiFe] hydrogenase by site-directed mutagenesis.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:11625-11630(1998).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS) OF 51-314 IN COMPLEX WITH HYDB AND
RP IRON-SULFUR CLUSTERS.
RX PubMed=15803334; DOI=10.1007/s00775-005-0632-x;
RA Volbeda A., Martin L., Cavazza C., Matho M., Faber B.W., Roseboom W.,
RA Albracht S.P., Garcin E., Rousset M., Fontecilla-Camps J.C.;
RT "Structural differences between the ready and unready oxidized states of
RT [NiFe] hydrogenases.";
RL J. Biol. Inorg. Chem. 10:239-249(2005).
CC -!- FUNCTION: Involved in hydrogen uptake for the anaerobic reduction of
CC sulfate to hydrogen sulfide in an electron transport chain. Cytochrome
CC c3 is the physiological electron acceptor.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2
CC H(+); Xref=Rhea:RHEA:20625, Rhea:RHEA-COMP:11576, Rhea:RHEA-
CC COMP:11577, ChEBI:CHEBI:15378, ChEBI:CHEBI:18276, ChEBI:CHEBI:29033,
CC ChEBI:CHEBI:29034; EC=1.12.2.1;
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Note=Binds 2 [4Fe-4S] clusters per subunit.;
CC -!- COFACTOR:
CC Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
CC Note=Binds 1 [3Fe-4S] cluster per subunit.;
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Redox potential:
CC E(0) is about +65 mV for the 3Fe-4S, and -340 mV for the 4Fe-4S
CC clusters. {ECO:0000269|PubMed:9751716};
CC -!- SUBUNIT: Heterodimer of a large and a small subunit.
CC {ECO:0000269|PubMed:15803334, ECO:0000269|PubMed:9751716}.
CC -!- SUBCELLULAR LOCATION: Periplasm.
CC -!- PTM: Predicted to be exported by the Tat system. The position of the
CC signal peptide cleavage has been experimentally proven.
CC -!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit
CC family. {ECO:0000305}.
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DR EMBL; M35333; AAA23371.2; -; Genomic_DNA.
DR PIR; JQ0761; S08198.
DR PDB; 1FRF; X-ray; 2.70 A; S=51-161, S=163-314.
DR PDB; 1YQW; X-ray; 1.83 A; A/B/C=51-314.
DR PDB; 1YRQ; X-ray; 2.10 A; A/B/C/D/F/G=51-314.
DR PDB; 3CUR; X-ray; 2.40 A; A/B/C=51-314.
DR PDB; 3CUS; X-ray; 2.20 A; A/B/C=51-314.
DR PDB; 3H3X; X-ray; 2.70 A; A/B/C=51-314.
DR PDB; 4UCQ; X-ray; 2.60 A; A/B/C=51-314.
DR PDB; 4UCW; X-ray; 2.30 A; A/B/C=51-314.
DR PDB; 4UCX; X-ray; 1.95 A; A/B/C=51-314.
DR PDB; 4UE2; X-ray; 2.02 A; A/B/C=51-314.
DR PDB; 4UE6; X-ray; 2.30 A; A/B/C=51-314.
DR PDB; 4UEW; X-ray; 2.08 A; A/B/C=51-314.
DR PDB; 4UPE; X-ray; 1.80 A; A/B/C=50-314.
DR PDB; 4UPV; X-ray; 1.52 A; A/B=50-314.
DR PDB; 4UQL; X-ray; 1.22 A; A/B=50-314.
DR PDB; 4UQP; X-ray; 1.42 A; A/B=50-314.
DR PDB; 4URH; X-ray; 1.44 A; A/B/C=50-314.
DR PDBsum; 1FRF; -.
DR PDBsum; 1YQW; -.
DR PDBsum; 1YRQ; -.
DR PDBsum; 3CUR; -.
DR PDBsum; 3CUS; -.
DR PDBsum; 3H3X; -.
DR PDBsum; 4UCQ; -.
DR PDBsum; 4UCW; -.
DR PDBsum; 4UCX; -.
DR PDBsum; 4UE2; -.
DR PDBsum; 4UE6; -.
DR PDBsum; 4UEW; -.
DR PDBsum; 4UPE; -.
DR PDBsum; 4UPV; -.
DR PDBsum; 4UQL; -.
DR PDBsum; 4UQP; -.
DR PDBsum; 4URH; -.
DR AlphaFoldDB; P18187; -.
DR SMR; P18187; -.
DR DIP; DIP-6172N; -.
DR MINT; P18187; -.
DR BRENDA; 1.12.2.1; 1906.
DR EvolutionaryTrace; P18187; -.
DR GO; GO:0009375; C:ferredoxin hydrogenase complex; IEA:InterPro.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0051538; F:3 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0047806; F:cytochrome-c3 hydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0008901; F:ferredoxin hydrogenase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.700; -; 1.
DR Gene3D; 4.10.480.10; -; 1.
DR InterPro; IPR027394; Cytochrome-c3_hydrogenase_C.
DR InterPro; IPR006137; NADH_UbQ_OxRdtase-like_20kDa.
DR InterPro; IPR037148; NiFe-Hase_small_C_sf.
DR InterPro; IPR037024; NiFe_Hase_small_N_sf.
DR InterPro; IPR001821; NiFe_hydrogenase_ssu.
DR InterPro; IPR006311; TAT_signal.
DR InterPro; IPR019546; TAT_signal_bac_arc.
DR PANTHER; PTHR30013; PTHR30013; 1.
DR Pfam; PF14720; NiFe_hyd_SSU_C; 1.
DR Pfam; PF01058; Oxidored_q6; 1.
DR Pfam; PF10518; TAT_signal; 1.
DR PIRSF; PIRSF000310; NiFe_hyd_ssu; 1.
DR TIGRFAMs; TIGR00391; hydA; 1.
DR TIGRFAMs; TIGR01409; TAT_signal_seq; 1.
DR PROSITE; PS51318; TAT; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 3Fe-4S; 4Fe-4S; Direct protein sequencing; Iron; Iron-sulfur;
KW Metal-binding; Oxidoreductase; Periplasm; Signal.
FT SIGNAL 1..49
FT /note="Tat-type signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00648,
FT ECO:0000269|PubMed:2154378"
FT CHAIN 50..314
FT /note="Periplasmic [NiFe] hydrogenase small subunit"
FT /id="PRO_0000013415"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 164
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 197
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 234
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 237
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 262
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 268
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 277
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 295
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 298
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT MUTAGEN 238
FT /note="P->C: Decreased hydrogen uptake and increased
FT hydrogen production."
FT /evidence="ECO:0000269|PubMed:9751716"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 69..74
FT /evidence="ECO:0007829|PDB:4UQL"
FT TURN 78..81
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 82..88
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:4UQL"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 103..114
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 121..129
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 131..134
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 144..154
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 162..167
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 183..187
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 201..213
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 226..229
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 230..232
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 240..244
FT /evidence="ECO:0007829|PDB:4UQL"
FT STRAND 250..254
FT /evidence="ECO:0007829|PDB:4UE2"
FT HELIX 255..258
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 264..266
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 270..272
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 277..280
FT /evidence="ECO:0007829|PDB:4UQL"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:4UQL"
FT TURN 288..292
FT /evidence="ECO:0007829|PDB:4UQL"
FT HELIX 303..306
FT /evidence="ECO:0007829|PDB:4UQL"
SQ SEQUENCE 314 AA; 33621 MW; 48BE00FE51D23A68 CRC64;
MNFSVGLGRD DAEKRLVQNG VSRRDFMKFC ATVAAAMGMG PAFAPKVAEA LTAKHRPSVV
WLHNAECTGC TEAAIRTIKP YIDALILDTI SLDYQETIMA AAGEAAEAAL HQALEGKDGY
YLVVEGGLPT IDGGQWGMVA GHPMIETTKK AAAKAKGIIC IGTCSAYGGV QKAKPNPSQA
KGVSEALGVK TINIPGCPPN PINFVGAVVH VLTKGIPDLD ENGRPKLFYG ELVHDNCPRL
PHFEASEFAP SFDSEEAKKG FCLYELGCKG PVTYNNCPKV LFNQVNWPVQ AGHPCLGCSE
PDFWDTMTPF YEQG
