HYD2D_PYRFU
ID HYD2D_PYRFU Reviewed; 237 AA.
AC E7FHF8; Q7LWY7; Q9P9M5;
DT 09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 52.
DE RecName: Full=Sulfhydrogenase 2 subunit delta;
DE EC=1.12.1.5;
DE AltName: Full=Hydrogen dehydrogenase (NAD(P)(+));
DE AltName: Full=Hydrogenase-II subunit delta {ECO:0000303|PubMed:10714990};
DE Short=H-II delta {ECO:0000303|PubMed:10714990};
DE AltName: Full=NADP-reducing hydrogenase subunit ShyD;
DE AltName: Full=Sulfhydrogenase II subunit delta {ECO:0000303|PubMed:10714990};
GN Name=shyD {ECO:0000312|EMBL:AAF61853.1}; OrderedLocusNames=PF1331;
OS Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=186497;
RN [1] {ECO:0000305, ECO:0000312|EMBL:AAF61853.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-13, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR
RP LOCATION, SUBUNIT, AND EPR SPECTROSCOPY.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000312|EMBL:AAF61853.1};
RX PubMed=10714990; DOI=10.1128/jb.182.7.1864-1871.2000;
RA Ma K., Weiss R., Adams M.W.;
RT "Characterization of hydrogenase II from the hyperthermophilic archaeon
RT Pyrococcus furiosus and assessment of its role in sulfur reduction.";
RL J. Bacteriol. 182:1864-1871(2000).
RN [2] {ECO:0000312|EMBL:AAL81455.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
RX PubMed=10430560; DOI=10.1093/genetics/152.4.1299;
RA Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
RA DiRuggiero J., Robb F.T.;
RT "Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P.
RT horikoshii inferred from complete genomic sequences.";
RL Genetics 152:1299-1305(1999).
RN [3] {ECO:0000305}
RP FUNCTION.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000269|PubMed:11133967};
RX PubMed=11133967; DOI=10.1128/jb.183.2.716-724.2001;
RA Adams M.W., Holden J.F., Menon A.L., Schut G.J., Grunden A.M., Hou C.,
RA Hutchins A.M., Jenney F.E. Jr., Kim C., Ma K., Pan G., Roy R., Sapra R.,
RA Story S.V., Verhagen M.F.;
RT "Key role for sulfur in peptide metabolism and in regulation of three
RT hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus.";
RL J. Bacteriol. 183:716-724(2001).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000269|PubMed:11265463};
RX PubMed=11265463; DOI=10.1016/s0076-6879(01)31059-5;
RA Ma K., Adams M.W.;
RT "Hydrogenases I and II from Pyrococcus furiosus.";
RL Methods Enzymol. 331:208-216(2001).
CC -!- FUNCTION: Part of a bifunctional enzyme complex that functions as a
CC hydrogen-evolving hydrogenase with sulfur-reducing activity. May play a
CC role in hydrogen cycling during fermentative growth. Activity exhibited
CC with NAD in addition to NADPH. The alpha and delta subunits form the
CC hydrogenase component that catalyzes the reduction of protons to evolve
CC hydrogen. {ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11133967,
CC ECO:0000269|PubMed:11265463}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2 + NADP(+) = H(+) + NADPH; Xref=Rhea:RHEA:18637,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:18276, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349; EC=1.12.1.5;
CC Evidence={ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11265463};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2 + NAD(+) = H(+) + NADH; Xref=Rhea:RHEA:24636,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:18276, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.12.1.5;
CC Evidence={ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11265463};
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:10714990};
CC Note=Binds 1 nickel ion per subunit. {ECO:0000269|PubMed:10714990};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:10714990};
CC Note=Binds 2 [4Fe-4S] clusters. {ECO:0000269|PubMed:10714990};
CC -!- COFACTOR:
CC Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
CC Evidence={ECO:0000269|PubMed:10714990};
CC Note=Binds 1 [3Fe-4S] cluster. {ECO:0000269|PubMed:10714990};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.25 mM for methyl viologen (sodium dithionate and H(+) as
CC cosubstrates) {ECO:0000269|PubMed:10714990};
CC KM=1.0 mM for methyl viologen (H(2) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=0.13 mM for H(2) (methyl viologen as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=63 uM for NADPH (H(+) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=71 uM for NADH (H(+) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=17 uM for NADP (H(2) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=125 uM for NAD (H(2) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=0.2 mM for sulfur (H(2) as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC KM=0.67 mM for polysulfide (NADPH as cosubstrate)
CC {ECO:0000269|PubMed:10714990};
CC Note=Measured for the whole complex. {ECO:0000269|PubMed:10714990};
CC pH dependence:
CC Optimum pH is 8 for hydrogenase activity at >95 degrees Celsius.
CC {ECO:0000269|PubMed:10714990};
CC Temperature dependence:
CC Optimum temperature is greater than 90 degrees Celsius. Activity
CC increases with increasing temperature from 30 degrees Celsius to 90
CC degrees Celsius. Has a half-life of 6 hours at 95 degrees Celsius.
CC {ECO:0000269|PubMed:10714990};
CC -!- SUBUNIT: Dimer of heterotetramer of alpha, beta, gamma and delta
CC subunits. The nickel-containing alpha and delta subunits constitute the
CC hydrogenase activity. The beta and gamma subunits (flavin-containing
CC dimer) constitute the sulfur reductase activity.
CC {ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11265463}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10714990}.
CC -!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit
CC family. {ECO:0000255}.
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DR EMBL; AF176650; AAF61853.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL81455.1; -; Genomic_DNA.
DR RefSeq; WP_011012477.1; NC_018092.1.
DR AlphaFoldDB; E7FHF8; -.
DR SMR; E7FHF8; -.
DR STRING; 186497.PF1331; -.
DR PRIDE; E7FHF8; -.
DR EnsemblBacteria; AAL81455; AAL81455; PF1331.
DR GeneID; 41713134; -.
DR KEGG; pfu:PF1331; -.
DR PATRIC; fig|186497.12.peg.1394; -.
DR eggNOG; arCOG02472; Archaea.
DR HOGENOM; CLU_053270_0_0_2; -.
DR OMA; CKLNEYE; -.
DR OrthoDB; 44934at2157; -.
DR PhylomeDB; E7FHF8; -.
DR BioCyc; MetaCyc:MON-17853; -.
DR BRENDA; 1.12.1.5; 5243.
DR BRENDA; 1.12.98.4; 5243.
DR Proteomes; UP000001013; Chromosome.
DR GO; GO:0005737; C:cytoplasm; 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:0050583; F:hydrogen dehydrogenase (NADP+) activity; IEA:RHEA.
DR GO; GO:0047985; F:hydrogen dehydrogenase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.700; -; 1.
DR InterPro; IPR006137; NADH_UbQ_OxRdtase-like_20kDa.
DR InterPro; IPR037024; NiFe_Hase_small_N_sf.
DR Pfam; PF01058; Oxidored_q6; 1.
PE 1: Evidence at protein level;
KW 3Fe-4S; 4Fe-4S; Cytoplasm; Direct protein sequencing; Iron; Iron-sulfur;
KW Metal-binding; NAD; NADP; Nickel; Oxidoreductase; Reference proteome.
FT CHAIN 1..237
FT /note="Sulfhydrogenase 2 subunit delta"
FT /id="PRO_0000420726"
FT BINDING 11
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 14
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 83
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 132
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 160
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 163
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 170
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 179
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 188
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 192
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 199
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P21853"
FT BINDING 202
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P21853"
SQ SEQUENCE 237 AA; 26285 MW; C2BFF006B37EC09F CRC64;
MKLGVFELTD CGGCALNLLF LYDKLLDLLE FYEIAEFHMA TSKKSREKID VALVTGTVST
QRDLEVLRDA RNRSEYLIAL GTCATHGSVQ GVIENSKEAY RRVYGNGKPP VKLLNPKPVT
DYVPVDFAIP GCPYDKEEVF QVLIDIAKGI EPVAKDYPVC LECKLNEYEC VLLKKRIPCL
GPVTAGGCNA KCPSYGLGCI GCRGPSLDNN VPGMFEVLKE ILPDEEIARK LRTFARW
