ID   PHNL_DESVM              Reviewed;         567 AA.
AC   P21852; B8DPE0;
DT   01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT   14-APR-2009, sequence version 2.
DT   27-MAR-2024, entry version 142.
DE   RecName: Full=Periplasmic [NiFe] hydrogenase large subunit;
DE            EC=1.12.2.1;
DE   AltName: Full=NiFe hydrogenlyase large chain;
DE   Flags: Precursor;
GN   Name=hydB; OrderedLocusNames=DvMF_0270;
OS   Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F).
OC   Bacteria; Thermodesulfobacteriota; Desulfovibrionia; Desulfovibrionales;
OC   Desulfovibrionaceae; Nitratidesulfovibrio.
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] {ECO:0007744|PDB:1H2A}
RP   X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552, AND COFACTOR.
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] {ECO:0007744|PDB:1H2R}
RP   X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS), AND COFACTOR.
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=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC         Evidence={ECO:0000269|PubMed:10378274, ECO:0000269|PubMed:9438867};
CC   -!- COFACTOR:
CC       Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC         Evidence={ECO:0000269|PubMed:10378274, ECO:0000269|PubMed:9438867};
CC   -!- SUBUNIT: Heterodimer of a large and a small subunit.
CC   -!- SUBCELLULAR LOCATION: Periplasm.
CC   -!- MISCELLANEOUS: Perhaps the leader of the small subunit serves as a
CC       transport vehicle for both subunits.
CC   -!- SIMILARITY: Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit
CC       family. {ECO:0000305}.
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DR   EMBL; M58339; AAA23370.1; -; Genomic_DNA.
DR   EMBL; CP001197; ACL07227.1; -; Genomic_DNA.
DR   PIR; B45865; B45865.
DR   PDB; 1H2A; X-ray; 1.80 A; L=1-567.
DR   PDB; 1H2R; X-ray; 1.40 A; L=19-552.
DR   PDB; 1UBH; X-ray; 1.35 A; L=19-552.
DR   PDB; 1UBJ; X-ray; 1.35 A; L=19-552.
DR   PDB; 1UBK; X-ray; 1.18 A; L=19-552.
DR   PDB; 1UBL; X-ray; 1.20 A; L=19-552.
DR   PDB; 1UBM; X-ray; 1.40 A; L=19-552.
DR   PDB; 1UBO; X-ray; 1.35 A; L=19-552.
DR   PDB; 1UBR; X-ray; 1.34 A; L=19-552.
DR   PDB; 1UBT; X-ray; 1.34 A; L=19-552.
DR   PDB; 1UBU; X-ray; 1.35 A; L=19-552.
DR   PDB; 1WUH; X-ray; 1.24 A; L=19-552.
DR   PDB; 1WUI; X-ray; 1.04 A; L=19-552.
DR   PDB; 1WUJ; X-ray; 1.40 A; L=19-552.
DR   PDB; 1WUK; X-ray; 1.10 A; L=19-552.
DR   PDB; 1WUL; X-ray; 1.50 A; L=19-552.
DR   PDB; 4U9H; X-ray; 0.89 A; L=20-552.
DR   PDB; 4U9I; X-ray; 1.06 A; L=20-552.
DR   PDB; 5XLE; X-ray; 1.69 A; L=1-552.
DR   PDB; 5XLF; X-ray; 1.71 A; L=1-552.
DR   PDB; 5XLG; X-ray; 1.64 A; L=1-552.
DR   PDB; 5XLH; X-ray; 1.93 A; L=1-552.
DR   PDB; 5Y4N; X-ray; 1.69 A; L=1-552.
DR   PDB; 8W6X; Other; 1.04 A; L=20-552.
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   PDBsum; 8W6X; -.
DR   AlphaFoldDB; P21852; -.
DR   SMR; P21852; -.
DR   DIP; DIP-41378N; -.
DR   IntAct; P21852; 1.
DR   MINT; P21852; -.
DR   STRING; 883.DvMF_0270; -.
DR   KEGG; dvm:DvMF_0270; -.
DR   eggNOG; COG0374; Bacteria.
DR   HOGENOM; CLU_030087_0_0_7; -.
DR   OrthoDB; 9761717at2; -.
DR   EvolutionaryTrace; P21852; -.
DR   GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
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:0016151; F:nickel cation binding; IEA:InterPro.
DR   Gene3D; 1.10.645.10; Cytochrome-c3 Hydrogenase, chain B; 1.
DR   InterPro; IPR001501; Ni-dep_hyd_lsu.
DR   InterPro; IPR018194; Ni-dep_hyd_lsu_Ni_BS.
DR   InterPro; IPR029014; NiFe-Hase_large.
DR   PANTHER; PTHR42958; HYDROGENASE-2 LARGE CHAIN; 1.
DR   PANTHER; PTHR42958:SF2; UPTAKE HYDROGENASE LARGE SUBUNIT; 1.
DR   Pfam; PF00374; NiFeSe_Hases; 1.
DR   SUPFAM; SSF56762; HydB/Nqo4-like; 1.
DR   PROSITE; PS00507; NI_HGENASE_L_1; 1.
DR   PROSITE; PS00508; NI_HGENASE_L_2; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Iron; Magnesium; Metal-binding; Nickel; Oxidoreductase;
KW   Periplasm.
FT   CHAIN           1..552
FT                   /note="Periplasmic [NiFe] hydrogenase large subunit"
FT                   /id="PRO_0000013405"
FT   PROPEP          553..567
FT                   /id="PRO_0000013406"
FT   BINDING         62
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         81
FT                   /ligand="Ni(2+)"
FT                   /ligand_id="ChEBI:CHEBI:49786"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         84
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         84
FT                   /ligand="Ni(2+)"
FT                   /ligand_id="ChEBI:CHEBI:49786"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         498
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         546
FT                   /ligand="Ni(2+)"
FT                   /ligand_id="ChEBI:CHEBI:49786"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         549
FT                   /ligand="Fe cation"
FT                   /ligand_id="ChEBI:CHEBI:24875"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         549
FT                   /ligand="Ni(2+)"
FT                   /ligand_id="ChEBI:CHEBI:49786"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   BINDING         552
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000269|PubMed:10378274,
FT                   ECO:0000269|PubMed:9438867, ECO:0007744|PDB:1H2A,
FT                   ECO:0007744|PDB:1H2R"
FT   CONFLICT        180
FT                   /note="S -> T (in Ref. 1; AAA23370)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        514..515
FT                   /note="KL -> NV (in Ref. 1; AAA23370)"
FT                   /evidence="ECO:0000305"
FT   STRAND          23..29
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          32..35
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          37..44
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          47..55
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           61..65
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           70..72
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           73..78
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          82..84
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           87..100
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           106..130
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           133..135
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           140..144
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           147..157
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          158..160
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           164..179
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           184..186
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   TURN            190..193
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           202..230
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          233..235
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           247..250
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           252..271
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           273..283
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           284..289
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          296..305
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           309..311
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          312..320
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           324..326
FT                   /evidence="ECO:0007829|PDB:1UBT"
FT   HELIX           332..334
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          335..338
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   TURN            340..343
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          344..347
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           352..354
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           366..368
FT                   /evidence="ECO:0007829|PDB:4U9I"
FT   STRAND          371..373
FT                   /evidence="ECO:0007829|PDB:1WUI"
FT   STRAND          375..378
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           387..396
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           400..413
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           417..420
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           423..453
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          467..477
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          480..489
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          492..499
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           501..506
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           517..522
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   STRAND          530..532
FT                   /evidence="ECO:0007829|PDB:1H2R"
FT   HELIX           534..542
FT                   /evidence="ECO:0007829|PDB:4U9H"
FT   HELIX           547..551
FT                   /evidence="ECO:0007829|PDB:4U9H"
SQ   SEQUENCE   567 AA;  62641 MW;  8BE92277C0E46FDA CRC64;
     MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN AYSSSTLFRG
     LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV GVHIPKNATY IRNLVLGAQY
     LHDHIVHFYH LHALDFVDVT AALKADPAKA AKVASSISPR KTTAADLKAV QDKLKTFVES
     GQLGPFTNAY FLGGHPAYYL DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV
     VGGVTCYDAL TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG
     EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR HPWKGQTQPK
     YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP KVKAVTDAVL AKLGVGPEAL
     FSTLGRTAAR GIETAVIAEY VGVMLQEYKD NIAKGDNVIC APWEMPKQAE GVGFVNAPRG
     GLSHWIRIED GKIGNFQLVV PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV
     HSFDPCIACG VHVIDGHTNE VHKFRIL
//