HYD1D_PYRFU
ID HYD1D_PYRFU Reviewed; 261 AA.
AC E7FHU4; Q59669; Q7LWZ9;
DT 09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
DT 08-MAR-2011, sequence version 1.
DT 03-AUG-2022, entry version 56.
DE RecName: Full=Sulfhydrogenase 1 subunit delta;
DE EC=1.12.1.3 {ECO:0000269|Ref.4};
DE AltName: Full=Hydrogenase I small subunit {ECO:0000303|PubMed:7704275};
DE AltName: Full=NADP-reducing hydrogenase subunit HydD {ECO:0000250|UniProtKB:Q46505, ECO:0000303|PubMed:7704275};
DE AltName: Full=Sulfhydrogenase I subunit delta {ECO:0000303|PubMed:7704275};
GN Name=hydD {ECO:0000303|PubMed:7704275}; OrderedLocusNames=PF0893;
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:CAA53036.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-37, FUNCTION,
RP SUBCELLULAR LOCATION, AND SUBUNIT.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000312|EMBL:CAA53036.1};
RX PubMed=7704275; DOI=10.1099/13500872-141-2-449;
RA Pedroni P., Della Volpe A., Galli G., Mura G.M., Pratesi C., Grandi G.;
RT "Characterization of the locus encoding the [Ni-Fe] sulfhydrogenase from
RT the archaeon Pyrococcus furiosus: evidence for a relationship to bacterial
RT sulfite reductases.";
RL Microbiology 141:449-458(1995).
RN [2] {ECO:0000312|EMBL:AAL81017.1}
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, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND EPR SPECTROSCOPY.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 {ECO:0000269|PubMed:2538471};
RX PubMed=2538471; DOI=10.1016/s0021-9258(18)83701-2;
RA Bryant F.O., Adams M.W.;
RT "Characterization of hydrogenase from the hyperthermophilic
RT archaebacterium, Pyrococcus furiosus.";
RL J. Biol. Chem. 264:5070-5079(1989).
RN [4] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 {ECO:0000269|Ref.4};
RX DOI=10.1111/j.1574-6968.1994.tb07175.x;
RA Ma K., Zhou Z.H., Adams M.W.;
RT "Hydrogen production from pyruvate by enzymes purified by the
RT hyperthermophilic archaeon Pyrococcus furiosus: A key role for NADPH.";
RL FEMS Microbiol. Lett. 122:245-250(1994).
RN [5] {ECO:0000305}
RP COFACTOR, SUBUNIT, AND EPR SPECTROSCOPY.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 {ECO:0000269|PubMed:7615063};
RX PubMed=7615063; DOI=10.1016/0014-5793(95)00622-g;
RA Arendsen A.F., Veenhuizen P.T., Hagen W.R.;
RT "Redox properties of the sulfhydrogenase from Pyrococcus furiosus.";
RL FEBS Lett. 368:117-121(1995).
RN [6] {ECO:0000305}
RP FUNCTION, COFACTOR, AND EPR SPECTROSCOPY.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000269|PubMed:10439073};
RX PubMed=10439073; DOI=10.1007/s007750050314;
RA Silva P.J., de Castro B., Hagen W.R.;
RT "On the prosthetic groups of the NiFe sulfhydrogenase from Pyrococcus
RT furiosus: topology, structure, and temperature-dependent redox chemistry.";
RL J. Biol. Inorg. Chem. 4:284-291(1999).
RN [7] {ECO:0000305}
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
RC {ECO:0000269|PubMed:11054105};
RX PubMed=11054105; DOI=10.1046/j.1432-1327.2000.01745.x;
RA Silva P.J., van den Ban E.C., Wassink H., Haaker H., de Castro B.,
RA Robb F.T., Hagen W.R.;
RT "Enzymes of hydrogen metabolism in Pyrococcus furiosus.";
RL Eur. J. Biochem. 267:6541-6551(2000).
RN [8] {ECO:0000305}
RP FUNCTION, AND CATALYTIC ACTIVITY.
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 an
CC NADPH-dependent hydrogen-evolving hydrogenase with sulfur reducing
CC activity. May play a role in hydrogen cycling during fermentative
CC growth. Activity not exhibited with NAD. The alpha and delta subunits
CC form the hydrogenase component that catalyzes the reduction of protons
CC to evolve hydrogen. {ECO:0000269|PubMed:10439073,
CC ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:11265463,
CC ECO:0000269|PubMed:2538471, ECO:0000269|PubMed:7704275,
CC ECO:0000269|Ref.4}.
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=1.12.1.3;
CC Evidence={ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:11265463,
CC ECO:0000269|Ref.4};
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:10439073, ECO:0000269|PubMed:2538471,
CC ECO:0000269|PubMed:7615063};
CC Note=Binds 1 nickel ion per tetramer. {ECO:0000269|PubMed:10439073,
CC ECO:0000269|PubMed:2538471, ECO:0000269|PubMed:7615063};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:10439073, ECO:0000269|PubMed:7615063};
CC Note=Binds 2 [4Fe-4S] clusters. {ECO:0000269|PubMed:10439073,
CC ECO:0000269|PubMed:7615063};
CC -!- COFACTOR:
CC Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
CC Evidence={ECO:0000269|PubMed:10439073};
CC Note=Binds 1 [3Fe-4S] cluster. {ECO:0000269|PubMed:10439073};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.3 mM for methyl viologen {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC KM=79 uM for ferredoxin {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC KM=0.08 mM for methylene blue {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC KM=70 uM for ferredoxin (sodium dithionate as cosubstrate)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC KM=1.0 uM for ferredoxin (pyruvate and NADP as cosubstrates)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC KM=40 uM for NADP (pure H(2) as cosubstrate)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC KM=0.2 mM for NADPH (H(+) as cosubstrate)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC KM=3.0 mM for NADH (H(+) as cosubstrate)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC KM=5.0 mM for methyl viologen (H(2) as cosubstrate)
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|PubMed:7615063, ECO:0000269|Ref.4};
CC Vmax=2900 umol/min/mg enzyme with methyl viologen as substrate
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC Vmax=18 umol/min/mg enzyme with ferredoxin as substrate (pyruvate and
CC NADP as cosubstrates) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Vmax=250 umol/min/mg enzyme with ferredoxin as substrate
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC Vmax=261 umol/min/mg enzyme with methylene blue as substrate
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC Vmax=67 umol/min/mg enzyme with ferredoxin as substrate (sodium
CC dithionate as cosubstrate) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Vmax=75 umol/min/mg enzyme with NADP as substrate (pure H(2) as
CC cosubstrate) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Vmax=10 umol/min/mg enzyme with NADPH as substrate (H(+) as
CC cosubstrate) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Vmax=6 umol/min/mg enzyme with NADPH as substrate (H(+) as electron
CC acceptor) {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC Vmax=1.6 umol/min/mg enzyme with NADH as substrate (H(+) as
CC cosubstrate) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Vmax=250 umol/min/mg enzyme with methyl viologen as substrate (H(2)
CC as cosubstrate) {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC Note=Measured for the whole complex. {ECO:0000269|PubMed:11054105,
CC ECO:0000269|PubMed:2538471, ECO:0000269|Ref.4};
CC pH dependence:
CC Optimum pH is 8 for hydrogenase activity at >95 degrees Celsius.
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC Temperature dependence:
CC Optimum temperature is greater than 95 degrees Celsius for
CC hydrogenase activity. Stable up to 100 degrees Celsius. Loses 50% of
CC activity at 80 degrees Celsius after 21 hour incubation.
CC {ECO:0000269|PubMed:11054105, ECO:0000269|PubMed:2538471,
CC ECO:0000269|Ref.4};
CC -!- SUBUNIT: Heterotetramer of alpha, beta, gamma and delta subunits. The
CC nickel-containing alpha and delta subunits constitute the hydrogenase
CC activity. The beta and gamma subunits (flavin-containing dimer)
CC constitute the sulfur reductase activity. {ECO:0000269|PubMed:7615063,
CC ECO:0000269|PubMed:7704275}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:7704275,
CC ECO:0000269|Ref.4}.
CC -!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase small subunit
CC family. {ECO:0000255}.
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DR EMBL; X75255; CAA53036.1; -; Genomic_DNA.
DR EMBL; AE009950; AAL81017.1; -; Genomic_DNA.
DR PIR; S48835; S48835.
DR RefSeq; WP_011012028.1; NC_018092.1.
DR AlphaFoldDB; E7FHU4; -.
DR SMR; E7FHU4; -.
DR STRING; 186497.PF0893; -.
DR PRIDE; E7FHU4; -.
DR EnsemblBacteria; AAL81017; AAL81017; PF0893.
DR GeneID; 41712701; -.
DR KEGG; pfu:PF0893; -.
DR PATRIC; fig|186497.12.peg.944; -.
DR eggNOG; arCOG02472; Archaea.
DR HOGENOM; CLU_053270_0_0_2; -.
DR OMA; GSWPEDI; -.
DR OrthoDB; 44934at2157; -.
DR PhylomeDB; E7FHU4; -.
DR BioCyc; MetaCyc:MON-16384; -.
DR BRENDA; 1.12.1.3; 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:UniProtKB-EC.
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; NADP; Nickel; Oxidoreductase; Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7704275"
FT CHAIN 2..261
FT /note="Sulfhydrogenase 1 subunit delta"
FT /id="PRO_0000420724"
FT BINDING 14
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 17
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 86
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 136
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 164
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 167
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 174
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 183
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 192
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 196
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 203
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P12943"
FT BINDING 206
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000250|UniProtKB:P12943"
SQ SEQUENCE 261 AA; 29234 MW; 3B8D89AE42C88854 CRC64;
MGKVRIGFYA LTSCYGCQLQ LAMMDELLQL IPNAEIVCWF MIDRDSIEDE KVDIAFIEGS
VSTEEEVELV KKIRENAKIV VAVGACAVQG GVQSWSEKPL EELWKKVYGD AKVKFQPKKA
EPVSKYIKVD YNIYGCPPEK KDFLYALGTF LIGSWPEDID YPVCLECRLN GHPCILLEKG
EPCLGPVTRA GCNARCPGFG VACIGCRGAI GYDVAWFDSL AKVFKEKGMT KEEIIERMKM
FNGHDERVEK MVEKIFSGGE Q
