NIFD_KLEPN
ID NIFD_KLEPN Reviewed; 483 AA.
AC P00466; P09770;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1989, sequence version 2.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Nitrogenase molybdenum-iron protein alpha chain;
DE EC=1.18.6.1;
DE AltName: Full=Dinitrogenase;
DE AltName: Full=Nitrogenase component I;
GN Name=nifD;
OS Klebsiella pneumoniae.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Klebsiella/Raoultella group; Klebsiella.
OX NCBI_TaxID=573;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3062178; DOI=10.1016/0022-2836(88)90205-7;
RA Arnold W., Rump A., Klipp W., Priefer U.B., Puehler A.;
RT "Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire
RT nitrogen fixation gene cluster of Klebsiella pneumoniae.";
RL J. Mol. Biol. 203:715-738(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Arnold W.;
RL Submitted (JAN-1989) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3043382; DOI=10.1093/nar/16.14.7199;
RA Steinbauer J., Wenzel W., Hess D.;
RT "Nucleotide and deduced amino acid sequences of the Klebsiella pneumoniae
RT nifK gene coding for the beta-subunit of nitrogenase MoFe protein.";
RL Nucleic Acids Res. 16:7199-7199(1988).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=MSAL;
RX PubMed=3322262; DOI=10.1042/bj2470287;
RA Ioannidis I., Buck M.;
RT "Nucleotide sequence of the Klebsiella pneumoniae nifD gene and predicted
RT amino acid sequence of the alpha-subunit of nitrogenase MoFe protein.";
RL Biochem. J. 247:287-291(1987).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-207.
RC STRAIN=UNF 841;
RX PubMed=6809876;
RA Scott K.F., Rolfe B.G., Shine J.;
RT "Biological nitrogen fixation: primary structure of the Klebsiella
RT pneumoniae nifH and nifD genes.";
RL J. Mol. Appl. Genet. 1:71-81(1981).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 207-483.
RX PubMed=3211766; DOI=10.1093/nar/16.24.11843;
RA Lignon J.M., Nakas J.P.;
RT "Nucleotide sequence of nifK and partial sequence of nifD from Frankia
RT species strain FaC1.";
RL Nucleic Acids Res. 16:11843-11843(1988).
RN [7]
RP ERRATUM OF PUBMED:3211766, AND CORRECTION OF ORGANISM GIVEN IN
RP PUBMED:3211766.
RA Lignon J.M., Nakas J.P.;
RL Nucleic Acids Res. 18:1097-1097(1990).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 452-483.
RX PubMed=3322261; DOI=10.1042/bj2470277;
RA Holland D., Zilberstein A., Zamir A., Sussman J.L.;
RT "A quantitative approach to sequence comparisons of nitrogenase MoFe
RT protein alpha- and beta-subunits including the newly sequenced nifK gene
RT from Klebsiella pneumoniae.";
RL Biochem. J. 247:277-285(1987).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 3-480 IN COMPLEX WITH 8FE-7S
RP CLUSTER AND 7FE-MO-9S-C-HOMOCITRYL CLUSTER, COFACTOR, AND SUBUNIT.
RX PubMed=10525412; DOI=10.1006/jmbi.1999.3107;
RA Mayer S.M., Lawson D.M., Gormal C.A., Roe S.M., Smith B.E.;
RT "New insights into structure-function relationships in nitrogenase: a 1.6 A
RT resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-
RT protein.";
RL J. Mol. Biol. 292:871-891(1999).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 3-483 IN COMPLEX WITH 8FE-7S
RP CLUSTER AND 7FE-MO-9S-C-HOMOCITRYL CLUSTER, COFACTOR, AND SUBUNIT.
RX PubMed=12133839; DOI=10.1074/jbc.m205888200;
RA Mayer S.M., Gormal C.A., Smith B.E., Lawson D.M.;
RT "Crystallographic analysis of the MoFe protein of nitrogenase from a nifV
RT mutant of Klebsiella pneumoniae identifies citrate as a ligand to the
RT molybdenum of iron molybdenum cofactor (FeMoco).";
RL J. Biol. Chem. 277:35263-35266(2002).
CC -!- FUNCTION: This molybdenum-iron protein is part of the nitrogenase
CC complex that catalyzes the key enzymatic reactions in nitrogen
CC fixation.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=16 ATP + 16 H2O + N2 + 8 reduced [2Fe-2S]-[ferredoxin] = 16
CC ADP + 6 H(+) + H2 + 2 NH4(+) + 8 oxidized [2Fe-2S]-[ferredoxin] + 16
CC phosphate; Xref=Rhea:RHEA:21448, Rhea:RHEA-COMP:10000, Rhea:RHEA-
CC COMP:10001, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17997,
CC ChEBI:CHEBI:18276, ChEBI:CHEBI:28938, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:33737, ChEBI:CHEBI:33738, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:456216; EC=1.18.6.1;
CC -!- COFACTOR:
CC Name=[8Fe-7S] cluster; Xref=ChEBI:CHEBI:21143;
CC Note=Binds 1 [8Fe-7S] cluster per heterodimer.;
CC -!- COFACTOR:
CC Name=[7Fe-Mo-9S-C-homocitryl] cluster; Xref=ChEBI:CHEBI:30409;
CC Note=Binds 1 [7Fe-Mo-9S-C-homocitryl] cluster per subunit.;
CC -!- SUBUNIT: Tetramer of two alpha and two beta chains. Forms complex with
CC the iron protein (nitrogenase component 2).
CC {ECO:0000269|PubMed:10525412, ECO:0000269|PubMed:12133839}.
CC -!- SIMILARITY: Belongs to the NifD/NifK/NifE/NifN family. {ECO:0000305}.
CC -!- CAUTION: The authors of PubMed:3211766 originally stated that their
CC sequence was from Frankia sp. {ECO:0000305}.
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DR EMBL; Y00316; CAA68413.1; -; Genomic_DNA.
DR EMBL; X07748; CAA30571.1; -; Genomic_DNA.
DR EMBL; X13303; CAA31667.1; -; Genomic_DNA.
DR EMBL; V00631; CAA23904.1; -; Genomic_DNA.
DR EMBL; X12649; CAA31179.1; -; Genomic_DNA.
DR EMBL; X06243; CAA29587.1; -; Genomic_DNA.
DR PIR; S01729; NIKBMA.
DR PDB; 1H1L; X-ray; 1.90 A; A/C=3-483.
DR PDB; 1QGU; X-ray; 1.60 A; A/C=3-480.
DR PDB; 1QH1; X-ray; 1.60 A; A/C=3-480.
DR PDB; 1QH8; X-ray; 1.60 A; A/C=3-480.
DR PDBsum; 1H1L; -.
DR PDBsum; 1QGU; -.
DR PDBsum; 1QH1; -.
DR PDBsum; 1QH8; -.
DR AlphaFoldDB; P00466; -.
DR SMR; P00466; -.
DR DIP; DIP-6206N; -.
DR BioCyc; MetaCyc:NIFDKLEB-MON; -.
DR BRENDA; 1.18.6.1; 2814.
DR EvolutionaryTrace; P00466; -.
DR GO; GO:0016612; C:molybdenum-iron nitrogenase complex; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0018697; F:carbonyl sulfide nitrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016163; F:nitrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR CDD; cd01976; Nitrogenase_MoFe_alpha; 1.
DR InterPro; IPR000510; Nase/OxRdtase_comp1.
DR InterPro; IPR010143; Nase_comp1_asu.
DR InterPro; IPR000318; Nase_comp1_CS.
DR InterPro; IPR005972; Nase_Mo-Fe_asu.
DR PANTHER; PTHR43457; PTHR43457; 1.
DR Pfam; PF00148; Oxidored_nitro; 1.
DR TIGRFAMs; TIGR01862; N2-ase-Ialpha; 1.
DR TIGRFAMs; TIGR01282; nifD; 1.
DR PROSITE; PS00699; NITROGENASE_1_1; 1.
DR PROSITE; PS00090; NITROGENASE_1_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Iron; Iron-sulfur; Metal-binding; Molybdenum;
KW Nitrogen fixation; Nucleotide-binding; Oxidoreductase.
FT CHAIN 1..483
FT /note="Nitrogenase molybdenum-iron protein alpha chain"
FT /id="PRO_0000153069"
FT BINDING 63
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 89
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 155
FT /ligand="[8Fe-7S] cluster"
FT /ligand_id="ChEBI:CHEBI:21143"
FT /ligand_note="ligand shared with beta chain"
FT BINDING 275
FT /ligand="[7Fe-Mo-9S-C-homocitryl] cluster"
FT /ligand_id="ChEBI:CHEBI:30409"
FT BINDING 442
FT /ligand="[7Fe-Mo-9S-C-homocitryl] cluster"
FT /ligand_id="ChEBI:CHEBI:30409"
FT CONFLICT 16
FT /note="E -> Q (in Ref. 4)"
FT /evidence="ECO:0000305"
FT CONFLICT 261..264
FT /note="EMEN -> GDGD (in Ref. 6; CAA31179)"
FT /evidence="ECO:0000305"
FT CONFLICT 288
FT /note="E -> D (in Ref. 6; CAA31179)"
FT /evidence="ECO:0000305"
FT CONFLICT 341..343
FT /note="KYR -> NIA (in Ref. 6; CAA31179)"
FT /evidence="ECO:0000305"
FT CONFLICT 349..361
FT /note="RKVLLYMGGLRPR -> LRCCSIWRLP (in Ref. 6; CAA31179)"
FT /evidence="ECO:0000305"
FT CONFLICT 355
FT /note="M -> I (in Ref. 2; CAA31667)"
FT /evidence="ECO:0000305"
FT CONFLICT 469
FT /note="N -> T (in Ref. 6; CAA31179)"
FT /evidence="ECO:0000305"
FT HELIX 5..18
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 23..29
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 30..32
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 64..68
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 69..73
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 79..87
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 88..92
FT /evidence="ECO:0007829|PDB:1QGU"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:1QGU"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 121..126
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 129..142
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 147..153
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 156..159
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 164..175
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 192..206
FT /evidence="ECO:0007829|PDB:1QGU"
FT TURN 207..213
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 222..228
FT /evidence="ECO:0007829|PDB:1QGU"
FT TURN 232..235
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 236..244
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 248..254
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 259..264
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 269..274
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 276..290
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 294..296
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 301..313
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 318..346
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 350..358
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 359..362
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 364..369
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 373..381
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 384..390
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 391..393
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 399..403
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 406..416
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 419..423
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 425..433
FT /evidence="ECO:0007829|PDB:1QGU"
FT STRAND 438..443
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 444..446
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 452..467
FT /evidence="ECO:0007829|PDB:1QGU"
FT HELIX 470..473
FT /evidence="ECO:0007829|PDB:1QGU"
SQ SEQUENCE 483 AA; 54158 MW; 4A2BA83B2C0C6EE7 CRC64;
MMTNATGERN LALIQEVLEV FPETARKERR KHMMVSDPKM KSVGKCIISN RKSQPGVMTV
RGCAYAGSKG VVFGPIKDMA HISHGPAGCG QYSRAERRNY YTGVSGVDSF GTLNFTSDFQ
ERDIVFGGDK KLSKLIEEME LLFPLTKGIT IQSECPVGLI GDDISAVANA SSKALDKPVI
PVRCEGFRGV SQSLGHHIAN DVVRDWILNN REGQPFETTP YDVAIIGDYN IGGDAWASRI
LLEEMGLRVV AQWSGDGTLV EMENTPFVKL NLVHCYRSMN YIARHMEEKH QIPWMEYNFF
GPTKIAESLR KIADQFDDTI RANAEAVIAR YEGQMAAIIA KYRPRLEGRK VLLYMGGLRP
RHVIGAYEDL GMEIIAAGYE FAHNDDYDRT LPDLKEGTLL FDDASSYELE AFVKALKPDL
IGSGIKEKYI FQKMGVPFRQ MHSWDYSGPY HGYDGFAIFA RDMDMTLNNP AWNELTAPWL
KSA
