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Sulfhydrogenase 2 subunit delta (EC 1.12.1.5) (Hydrogen dehydrogenase (NAD(P)( ))) (Hydrogenase-II subunit delta) (H-II delta) (NADP-reducing hydrogenase subunit ShyD) (Sulfhydrogenase II subunit delta)

 HYD2D_PYRFU             Reviewed;         237 AA.
E7FHF8; Q7LWY7; Q9P9M5;
09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
08-MAR-2011, sequence version 1.
23-MAY-2018, entry version 36.
RecName: Full=Sulfhydrogenase 2 subunit delta;
EC=1.12.1.5;
AltName: Full=Hydrogen dehydrogenase (NAD(P)(+));
AltName: Full=Hydrogenase-II subunit delta {ECO:0000303|PubMed:10714990};
Short=H-II delta {ECO:0000303|PubMed:10714990};
AltName: Full=NADP-reducing hydrogenase subunit ShyD;
AltName: Full=Sulfhydrogenase II subunit delta {ECO:0000303|PubMed:10714990};
Name=shyD {ECO:0000312|EMBL:AAF61853.1}; OrderedLocusNames=PF1331;
Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1).
Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
Pyrococcus.
NCBI_TaxID=186497;
[1] {ECO:0000305, ECO:0000312|EMBL:AAF61853.1}
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-13, FUNCTION,
CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES,
SUBCELLULAR LOCATION, SUBUNIT, AND EPR SPECTROSCOPY.
STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
{ECO:0000312|EMBL:AAF61853.1};
PubMed=10714990; DOI=10.1128/JB.182.7.1864-1871.2000;
Ma K., Weiss R., Adams M.W.;
"Characterization of hydrogenase II from the hyperthermophilic
archaeon Pyrococcus furiosus and assessment of its role in sulfur
reduction.";
J. Bacteriol. 182:1864-1871(2000).
[2] {ECO:0000312|EMBL:AAL81455.1}
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1;
PubMed=10430560;
Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M.,
DiRuggiero J., Robb F.T.;
"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and
P. horikoshii inferred from complete genomic sequences.";
Genetics 152:1299-1305(1999).
[3] {ECO:0000305}
FUNCTION.
STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
{ECO:0000269|PubMed:11133967};
PubMed=11133967; DOI=10.1128/JB.183.2.716-724.2001;
Adams M.W., Holden J.F., Menon A.L., Schut G.J., Grunden A.M., Hou C.,
Hutchins A.M., Jenney F.E. Jr., Kim C., Ma K., Pan G., Roy R.,
Sapra R., Story S.V., Verhagen M.F.;
"Key role for sulfur in peptide metabolism and in regulation of three
hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus.";
J. Bacteriol. 183:716-724(2001).
[4] {ECO:0000305}
FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
STRAIN=ATCC 43587 / DSM 3638 / JCM 8422 / Vc1
{ECO:0000269|PubMed:11265463};
PubMed=11265463; DOI=10.1016/S0076-6879(01)31059-5;
Ma K., Adams M.W.;
"Hydrogenases I and II from Pyrococcus furiosus.";
Methods Enzymol. 331:208-216(2001).
-!- FUNCTION: Part of a bifunctional enzyme complex that functions as
a hydrogen-evolving hydrogenase with sulfur-reducing activity. May
play a role in hydrogen cycling during fermentative growth.
Activity exhibited with NAD in addition to NADPH. The alpha and
delta subunits form the hydrogenase component that catalyzes the
reduction of protons to evolve hydrogen.
{ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11133967,
ECO:0000269|PubMed:11265463}.
-!- CATALYTIC ACTIVITY: H(2) + NAD(P)(+) = H(+) + NAD(P)H.
{ECO:0000269|PubMed:10714990, ECO:0000269|PubMed:11265463}.
-!- COFACTOR:
Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
Evidence={ECO:0000269|PubMed:10714990};
Note=Binds 1 nickel ion per subunit.
{ECO:0000269|PubMed:10714990};
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000269|PubMed:10714990};
Note=Binds 2 [4Fe-4S] clusters. {ECO:0000269|PubMed:10714990};
-!- COFACTOR:
Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
Evidence={ECO:0000269|PubMed:10714990};
Note=Binds 1 [3Fe-4S] cluster. {ECO:0000269|PubMed:10714990};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=1.25 mM for methyl viologen (sodium dithionate and H(+) as
cosubstrates) {ECO:0000269|PubMed:10714990};
KM=1.0 mM for methyl viologen (H(2) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=0.13 mM for H(2) (methyl viologen as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=63 uM for NADPH (H(+) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=71 uM for NADH (H(+) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=17 uM for NADP (H(2) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=125 uM for NAD (H(2) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=0.2 mM for sulfur (H(2) as cosubstrate)
{ECO:0000269|PubMed:10714990};
KM=0.67 mM for polysulfide (NADPH as cosubstrate)
{ECO:0000269|PubMed:10714990};
Note=Measured for the whole complex.
{ECO:0000269|PubMed:10714990};
pH dependence:
Optimum pH is 8 for hydrogenase activity at >95 degrees Celsius.
{ECO:0000269|PubMed:10714990};
Temperature dependence:
Optimum temperature is greater than 90 degrees Celsius. Activity
increases with increasing temperature from 30 degrees Celsius to
90 degrees Celsius. Has a half-life of 6 hours at 95 degrees
Celsius. {ECO:0000269|PubMed:10714990};
-!- SUBUNIT: Dimer of heterotetramer of alpha, beta, gamma and delta
subunits. The nickel-containing alpha and delta subunits
constitute the hydrogenase activity. The beta and gamma subunits
(flavin-containing dimer) constitute the sulfur reductase
activity. {ECO:0000269|PubMed:10714990,
ECO:0000269|PubMed:11265463}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10714990}.
-!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase small
subunit family. {ECO:0000255}.
-----------------------------------------------------------------------
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EMBL; AF176650; AAF61853.1; -; Genomic_DNA.
EMBL; AE009950; AAL81455.1; -; Genomic_DNA.
RefSeq; WP_011012477.1; NC_003413.1.
ProteinModelPortal; E7FHF8; -.
SMR; E7FHF8; -.
STRING; 186497.PF1331; -.
EnsemblBacteria; AAL81455; AAL81455; PF1331.
GeneID; 1469206; -.
KEGG; pfu:PF1331; -.
PATRIC; fig|186497.12.peg.1394; -.
eggNOG; arCOG02472; Archaea.
eggNOG; COG1941; LUCA.
HOGENOM; HOG000004874; -.
KO; K17994; -.
OMA; CKLNEYE; -.
OrthoDB; POG093Z08NK; -.
BioCyc; MetaCyc:MONOMER-17853; -.
BRENDA; 1.12.1.5; 5243.
BRENDA; 1.12.98.4; 5243.
Proteomes; UP000001013; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0051538; F:3 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
Gene3D; 3.40.50.700; -; 1.
InterPro; IPR006137; NADH_UbQ_OxRdtase-like_20kDa.
InterPro; IPR037024; NiFe_Hase_small_N_sf.
Pfam; PF01058; Oxidored_q6; 1.
1: Evidence at protein level;
3Fe-4S; 4Fe-4S; Complete proteome; Cytoplasm;
Direct protein sequencing; Iron; Iron-sulfur; Metal-binding; NAD;
NADP; Nickel; Oxidoreductase; Reference proteome.
CHAIN 1 237 Sulfhydrogenase 2 subunit delta.
/FTId=PRO_0000420726.
METAL 11 11 Iron-sulfur 1 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 14 14 Iron-sulfur 1 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 83 83 Iron-sulfur 1 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 132 132 Iron-sulfur 1 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 160 160 Iron-sulfur 2 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 163 163 Iron-sulfur 2 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 170 170 Iron-sulfur 2 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 179 179 Iron-sulfur 2 (4Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 188 188 Iron-sulfur 3 (3Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 192 192 Iron-sulfur 3 (3Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 199 199 Iron-sulfur 3 (3Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
METAL 202 202 Iron-sulfur 3 (3Fe-4S).
{ECO:0000250|UniProtKB:P21853}.
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


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