PHNL_MEGGA
ID PHNL_MEGGA Reviewed; 551 AA.
AC P12944;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 116.
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;
OS Megalodesulfovibrio gigas (Desulfovibrio gigas).
OC Bacteria; Proteobacteria; Deltaproteobacteria; Desulfovibrionales;
OC Desulfovibrionaceae; Megalodesulfovibrio.
OX NCBI_TaxID=879;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-31.
RX PubMed=3322743; DOI=10.1089/dna.1987.6.539;
RA Li C., Peck H.D. Jr., le Gall J., Przybyla A.E.;
RT "Cloning, characterization, and sequencing of the genes encoding the large
RT and small subunits of the periplasmic [NiFe]hydrogenase of Desulfovibrio
RT gigas.";
RL DNA 6:539-551(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND SEQUENCE REVISION.
RX PubMed=2651421; DOI=10.1128/jb.171.5.2894-2899.1989;
RA Voordouw G., Menon N.K., le Gall J., Choi E.S., Peck H.D. Jr.,
RA Przybyla A.E.;
RT "Analysis and comparison of nucleotide sequences encoding the genes for
RT [NiFe] and [NiFeSe] hydrogenases from Desulfovibrio gigas and Desulfovibrio
RT baculatus.";
RL J. Bacteriol. 171:2894-2899(1989).
RN [3]
RP PROTEIN SEQUENCE OF 2-30.
RX PubMed=3322275; DOI=10.1016/0006-291x(87)90376-7;
RA Prickril B.C., He S.H., Li C., Menon N.K., Choi E.S., Przybyla A.E.,
RA Dervartanian D.V., Peck H.D. Jr., Fauque G., le Gall J., Teixeira M.,
RA Moura I., Moura J.J.G., Patil D., Huynh B.H.;
RT "Identification of three classes of hydrogenase in the genus,
RT Desulfovibrio.";
RL Biochem. Biophys. Res. Commun. 149:369-377(1987).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).
RX PubMed=7854413; DOI=10.1038/373580a0;
RA Volbeda A., Charon M.-H., Piras C., Hatchikian E.C., Frey M.,
RA Fontecilla-Camps J.-C.;
RT "Crystal structure of the nickel-iron hydrogenase from Desulfovibrio
RT gigas.";
RL Nature 373:580-587(1995).
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 Note=Binds 1 nickel ion per subunit.;
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; M18083; AAA23378.1; ALT_SEQ; Genomic_DNA.
DR PIR; B32315; HQDVLG.
DR PDB; 1FRV; X-ray; 2.85 A; B/D=1-536.
DR PDB; 1YQ9; X-ray; 2.35 A; H/I=1-536.
DR PDB; 2FRV; X-ray; 2.54 A; B/D/F/H/J/L=1-536.
DR PDBsum; 1FRV; -.
DR PDBsum; 1YQ9; -.
DR PDBsum; 2FRV; -.
DR AlphaFoldDB; P12944; -.
DR SMR; P12944; -.
DR EvolutionaryTrace; P12944; -.
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; Direct protein sequencing; Metal-binding; Nickel;
KW Oxidoreductase; Periplasm.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:3322275,
FT ECO:0000269|PubMed:3322743"
FT CHAIN 2..536
FT /note="Periplasmic [NiFe] hydrogenase large subunit"
FT /id="PRO_0000013403"
FT PROPEP 537..551
FT /id="PRO_0000013404"
FT BINDING 65
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:7854413"
FT BINDING 68
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 530
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:7854413"
FT BINDING 533
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT STRAND 8..11
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 16..19
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 21..28
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 31..39
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 45..49
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 54..56
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 66..68
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 71..84
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 90..114
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 124..128
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 131..141
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 148..163
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 168..170
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 174..177
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 186..214
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 231..234
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 236..255
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 257..267
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 268..273
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 280..282
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 293..295
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 296..298
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 301..303
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 307..312
FT /evidence="ECO:0007829|PDB:2FRV"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 319..322
FT /evidence="ECO:0007829|PDB:1YQ9"
FT TURN 324..327
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 328..331
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 355..357
FT /evidence="ECO:0007829|PDB:1FRV"
FT STRAND 359..362
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 371..380
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 384..397
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 401..404
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 407..437
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 451..461
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 464..473
FT /evidence="ECO:0007829|PDB:1YQ9"
FT STRAND 476..483
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 485..490
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 501..506
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 518..526
FT /evidence="ECO:0007829|PDB:1YQ9"
FT HELIX 531..535
FT /evidence="ECO:0007829|PDB:1YQ9"
SQ SEQUENCE 551 AA; 61480 MW; 4CF99AD3F75189B0 CRC64;
MSEMQGNKIV VDPITRIEGH LRIEVEVEGG KIKNAWSMST LFRGLEMILK GRDPRDAQHF
TQRACGVCTY VHALASVRAV DNCVGVKIPE NATLMRNLTM GAQYMHDHLV HFYHLHALDW
VNVANALNAD PAKAARLAND LSPRKTTTES LKAVQAKVKA LVESGQLGIF TNAYFLGGHP
AYVLPAEVDL IATAHYLEAL RVQVKAARAM AIFGAKNPHT QFTVVGGCTN YDSLRPERIA
EFRKLYKEVR EFIEQVYITD LLAVAGFYKN WAGIGKTSNF LTCGEFPTDE YDLNSRYTPQ
GVIWGNDLSK VDDFNPDLIE EHVKYSWYEG ADAHHPYKGV TKPKWTEFHG EDRYSWMKAP
RYKGEAFEVG PLASVLVAYA KKHEPTVKAV DLVLKTLGVG PEALFSTLGR TAARGIQCLT
AAQEVEVWLD KLEANVKAGK DDLYTDWQYP TESQGVGFVN APRGMLSHWI VQRGGKIENF
QHVVPSTWNL GPRCAERKLS AVEQALIGTP IADPKRPVEI LRTVHSYDPC IACGVHVIDP
ESNQVHKFRI L
