PHNS_DESVM
ID PHNS_DESVM Reviewed; 317 AA.
AC P21853; B8DPE1;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1991, sequence version 1.
DT 03-AUG-2022, entry version 152.
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; OrderedLocusNames=DvMF_0271;
OS Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Desulfovibrio.
OX NCBI_TaxID=883;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2269874; DOI=10.1099/00221287-136-10-2021;
RA Deckers H.M., Wilson F.R., Voordouw G.;
RT "Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio
RT vulgaris Miyazaki F.";
RL J. Gen. Microbiol. 136:2021-2028(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 19637 / Miyazaki F;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C.,
RA Richardson P.;
RT "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'.";
RL Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RX PubMed=9438867; DOI=10.1016/s0969-2126(97)00313-4;
RA Higuchi Y., Yagi T., Yasuoka N.;
RT "Unusual ligand structure in Ni-Fe active center and an additional Mg site
RT in hydrogenase revealed by high resolution X-ray structure analysis.";
RL Structure 5:1671-1680(1997).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
RX PubMed=10378274; DOI=10.1016/s0969-2126(99)80071-9;
RA Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T.;
RT "Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe]
RT hydrogenase upon reduction with H2, as revealed by X-ray structure analysis
RT at 1.4 A resolution.";
RL Structure 7:549-556(1999).
CC -!- FUNCTION: Catalyzes the reversible oxidoreduction of molecular
CC hydrogen, in conjunction with a specific electron acceptor, cytochrome
CC c3.
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 -!- 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; M58339; AAA23369.1; -; Genomic_DNA.
DR EMBL; CP001197; ACL07228.1; -; Genomic_DNA.
DR PIR; A45865; A45865.
DR RefSeq; WP_012611422.1; NC_011769.1.
DR PDB; 1H2A; X-ray; 1.80 A; S=1-317.
DR PDB; 1H2R; X-ray; 1.40 A; S=51-317.
DR PDB; 1UBH; X-ray; 1.35 A; S=51-317.
DR PDB; 1UBJ; X-ray; 1.35 A; S=51-317.
DR PDB; 1UBK; X-ray; 1.18 A; S=51-317.
DR PDB; 1UBL; X-ray; 1.20 A; S=51-317.
DR PDB; 1UBM; X-ray; 1.40 A; S=51-317.
DR PDB; 1UBO; X-ray; 1.35 A; S=51-317.
DR PDB; 1UBR; X-ray; 1.34 A; S=51-317.
DR PDB; 1UBT; X-ray; 1.34 A; S=51-317.
DR PDB; 1UBU; X-ray; 1.35 A; S=51-317.
DR PDB; 1WUH; X-ray; 1.24 A; S=51-317.
DR PDB; 1WUI; X-ray; 1.04 A; S=51-317.
DR PDB; 1WUJ; X-ray; 1.40 A; S=51-317.
DR PDB; 1WUK; X-ray; 1.10 A; S=51-317.
DR PDB; 1WUL; X-ray; 1.50 A; S=51-317.
DR PDB; 4U9H; X-ray; 0.89 A; S=53-317.
DR PDB; 4U9I; X-ray; 1.06 A; S=53-317.
DR PDB; 5XLE; X-ray; 1.69 A; S=51-317.
DR PDB; 5XLF; X-ray; 1.71 A; S=51-317.
DR PDB; 5XLG; X-ray; 1.64 A; S=51-317.
DR PDB; 5XLH; X-ray; 1.93 A; S=51-317.
DR PDB; 5Y4N; X-ray; 1.69 A; S=51-317.
DR PDBsum; 1H2A; -.
DR PDBsum; 1H2R; -.
DR PDBsum; 1UBH; -.
DR PDBsum; 1UBJ; -.
DR PDBsum; 1UBK; -.
DR PDBsum; 1UBL; -.
DR PDBsum; 1UBM; -.
DR PDBsum; 1UBO; -.
DR PDBsum; 1UBR; -.
DR PDBsum; 1UBT; -.
DR PDBsum; 1UBU; -.
DR PDBsum; 1WUH; -.
DR PDBsum; 1WUI; -.
DR PDBsum; 1WUJ; -.
DR PDBsum; 1WUK; -.
DR PDBsum; 1WUL; -.
DR PDBsum; 4U9H; -.
DR PDBsum; 4U9I; -.
DR PDBsum; 5XLE; -.
DR PDBsum; 5XLF; -.
DR PDBsum; 5XLG; -.
DR PDBsum; 5XLH; -.
DR PDBsum; 5Y4N; -.
DR AlphaFoldDB; P21853; -.
DR SMR; P21853; -.
DR DIP; DIP-41377N; -.
DR IntAct; P21853; 1.
DR MINT; P21853; -.
DR STRING; 883.DvMF_0271; -.
DR EnsemblBacteria; ACL07228; ACL07228; DvMF_0271.
DR KEGG; dvm:DvMF_0271; -.
DR eggNOG; COG1740; Bacteria.
DR HOGENOM; CLU_046107_0_0_7; -.
DR OMA; RSFNAHN; -.
DR OrthoDB; 798037at2; -.
DR BRENDA; 1.12.2.1; 1914.
DR EvolutionaryTrace; P21853; -.
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 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; Iron; Iron-sulfur; Metal-binding;
KW Oxidoreductase; Periplasm; Signal.
FT SIGNAL 1..50
FT /note="Tat-type signal"
FT CHAIN 51..317
FT /note="Periplasmic [NiFe] hydrogenase small subunit"
FT /id="PRO_0000013419"
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 200
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT BINDING 238
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 241
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 266
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 272
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT BINDING 281
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 299
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT BINDING 302
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:1WUI"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 69..75
FT /evidence="ECO:0007829|PDB:4U9H"
FT TURN 78..81
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 82..87
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 91..94
FT /evidence="ECO:0007829|PDB:4U9H"
FT TURN 96..98
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 103..114
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 120..129
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 131..134
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 144..151
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 152..154
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 155..162
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 163..167
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 183..187
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 195..197
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 204..217
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 230..233
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 244..248
FT /evidence="ECO:0007829|PDB:4U9H"
FT STRAND 254..258
FT /evidence="ECO:0007829|PDB:1UBM"
FT HELIX 259..262
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 268..270
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 274..276
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 281..284
FT /evidence="ECO:0007829|PDB:4U9H"
FT TURN 287..289
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:4U9H"
FT HELIX 307..310
FT /evidence="ECO:0007829|PDB:4U9H"
SQ SEQUENCE 317 AA; 34113 MW; 2EAF2D471932C8A8 CRC64;
MKISIGLGKE GVEERLAERG VSRRDFLKFC TAIAVTMGMG PAFAPEVARA LMGPRRPSVV
YLHNAECTGC SESVLRAFEP YIDTLILDTL SLDYHETIMA AAGDAAEAAL EQAVNSPHGF
IAVVEGGIPT AANGIYGKVA NHTMLDICSR ILPKAQAVIA YGTCATFGGV QAAKPNPTGA
KGVNDALKHL GVKAINIAGC PPNPYNLVGT IVYYLKNKAA PELDSLNRPT MFFGQTVHEQ
CPRLPHFDAG EFAPSFESEE ARKGWCLYEL GCKGPVTMNN CPKIKFNQTN WPVDAGHPCI
GCSEPDFWDA MTPFYQN
