PHNS_MEGGA
ID PHNS_MEGGA Reviewed; 288 AA.
AC P12943;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1991, sequence version 2.
DT 03-AUG-2022, entry version 131.
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 Megalodesulfovibrio gigas (Desulfovibrio gigas).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Megalodesulfovibrio.
OX NCBI_TaxID=879;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 24-69.
RX PubMed=3322743; DOI=10.1089/dna.1987.6.539;
RA Li C., Peck H.D. Jr., le Gall J., Przybyla A.E.;
RT "Cloning, characterization, and sequencing of the genes encoding the large
RT and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio
RT gigas.";
RL DNA 6:539-551(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND SEQUENCE REVISION.
RX PubMed=2651421; DOI=10.1128/jb.171.5.2894-2899.1989;
RA Voordouw G., Menon N.K., le Gall J., Choi E.S., Peck H.D. Jr.,
RA Przybyla A.E.;
RT "Analysis and comparison of nucleotide sequences encoding the genes for
RT [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio
RT baculatus.";
RL J. Bacteriol. 171:2894-2899(1989).
RN [3]
RP PROTEIN SEQUENCE OF 25-58.
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 PROTEIN SEQUENCE OF 25-49.
RX PubMed=3134950; DOI=10.1016/0300-9084(88)90070-3;
RA Niviere V., Forget N., Bovier-Lapierre G.E., Bonicel J., Hatchikian C.;
RT "Isolation, amino acid analysis and N-terminal sequence determination of
RT the two subunits of the nickel-containing hydrogenase of Desulfovibrio
RT gigas.";
RL Biochimie 70:267-272(1988).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).
RX PubMed=7854413; DOI=10.1038/373580a0;
RA Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M.,
RA Fontecilla-Camps J.-C.;
RT "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio
RT gigas.";
RL Nature 373:580-587(1995).
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.;
CC -!- COFACTOR:
CC Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
CC Note=Binds 1 [3Fe-4S] cluster.;
CC -!- SUBUNIT: Heterodimer of a large and a small subunit.
CC -!- SUBCELLULAR LOCATION: Periplasm.
CC -!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit
CC family. {ECO:0000305}.
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DR EMBL; M18083; AAA23377.1; ALT_SEQ; Genomic_DNA.
DR PIR; A32315; HQDVSG.
DR PDB; 1FRV; X-ray; 2.85 A; A/C=25-288.
DR PDB; 1YQ9; X-ray; 2.35 A; A/B=25-288.
DR PDB; 2FRV; X-ray; 2.54 A; A/C/E/G/I/S=25-288.
DR PDBsum; 1FRV; -.
DR PDBsum; 1YQ9; -.
DR PDBsum; 2FRV; -.
DR AlphaFoldDB; P12943; -.
DR SMR; P12943; -.
DR EvolutionaryTrace; P12943; -.
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 PANTHER; PTHR30013; PTHR30013; 1.
DR Pfam; PF14720; NiFe_hyd_SSU_C; 1.
DR Pfam; PF01058; Oxidored_q6; 1.
DR PIRSF; PIRSF000310; NiFe_hyd_ssu; 1.
DR TIGRFAMs; TIGR00391; hydA; 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..23
FT /evidence="ECO:0000269|PubMed:3322743"
FT CHAIN 24..288
FT /note="Periplasmic [NiFe] hydrogenase small subunit"
FT /id="PRO_0000013416"
FT BINDING 41
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 44
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 136
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 172
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 209
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 212
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 243
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 252
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 270
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 273
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT CONFLICT 25..28
FT /note="LTAK -> SEMQ (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 47..48
FT /note="SL -> LV (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 48
FT /note="L -> V (in Ref. 1; AAA23377)"
FT /evidence="ECO:0000305"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 52..55
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 56..62
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 70..72
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 90..101
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 116..123
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 127..133
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 134..139
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 142..144
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 155..159
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 176..188
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 201..204
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:1FRV"
FT HELIX 230..233
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 252..255
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 258..260
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 263..267
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 278..281
FT /evidence="ECO:0007829|PDB:1YQ9"
SQ SEQUENCE 288 AA; 30816 MW; 4827967DA110AE94 CRC64;
MKFCTAVAVA MGMGPAFAPK VAEALTAKKR PSVVYLHNAE CTGCSESLLR TVDPYVDELI
LDVISMDYHE TLMAGAGHAV EEALHEAIKG DFVCVIEGGI PMGDGGYWGK VGRRNMYDIC
AEVAPKAKAV IAIGTCATYG GVQAAKPNPT GTVGVNEALG KLGVKAINIA GCPPNPMNFV
GTVVHLLTKG MPELDKQGRP VMFFGETVHD NCPRLKHFEA GEFATSFGSP EAKKGYCLYE
LGCKGPDTYN NCPKQLFNQV NWPVQAGHPC IACSEPNFWD LYSPFYSA
