PHNL_DESVM
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 03-AUG-2022, entry version 135.
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; 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) OF 19-552.
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=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
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 RefSeq; WP_012611421.1; NC_011769.1.
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 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; P21852; -.
DR SMR; P21852; -.
DR DIP; DIP-41378N; -.
DR IntAct; P21852; 1.
DR MINT; P21852; -.
DR STRING; 883.DvMF_0270; -.
DR EnsemblBacteria; ACL07227; ACL07227; DvMF_0270.
DR KEGG; dvm:DvMF_0270; -.
DR eggNOG; COG0374; Bacteria.
DR HOGENOM; CLU_030087_0_0_7; -.
DR OMA; EEVTHSW; -.
DR OrthoDB; 1967820at2; -.
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; -; 1.
DR InterPro; IPR001501; Ni-dep_hyd_lsu.
DR InterPro; IPR018194; Ni-dep_hyd_lsu_Ni_BS.
DR InterPro; IPR029014; NiFe-Hase_large.
DR Pfam; PF00374; NiFeSe_Hases; 1.
DR SUPFAM; SSF56762; SSF56762; 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 BINDING 81
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 84
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 84
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 498
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 546
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 549
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT BINDING 549
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 552
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
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
