NIFA_BRADU
ID NIFA_BRADU Reviewed; 582 AA.
AC P05407;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2003, sequence version 4.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Nif-specific regulatory protein;
GN Name=nifA; OrderedLocusNames=blr2037;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3313281; DOI=10.1093/nar/15.20.8479;
RA Thoeny B., Fischer H.-M., Anthamatten D., Bruderer T., Hennecke H.;
RT "The symbiotic nitrogen fixation regulatory operon (fixRnifA) of
RT Bradyrhizobium japonicum is expressed aerobically and is subject to a
RT novel, nifA-independent type of activation.";
RL Nucleic Acids Res. 15:8479-8499(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
RN [3]
RP METAL-BINDING.
RX PubMed=3357773; DOI=10.1093/nar/16.5.2207;
RA Fischer H.-M., Bruderer T., Hennecke H.;
RT "Essential and non-essential domains in the Bradyrhizobium japonicum NifA
RT protein: identification of indispensable cysteine residues potentially
RT involved in redox reactivity and/or metal binding.";
RL Nucleic Acids Res. 16:2207-2224(1988).
RN [4]
RP METAL-BINDING.
RX PubMed=2792368; DOI=10.1016/0014-5793(89)81083-x;
RA Fischer H.-M., Fritsche S., Herzog B., Hennecke H.;
RT "Critical spacing between two essential cysteine residues in the
RT interdomain linker of the Bradyrhizobium japonicum NifA protein.";
RL FEBS Lett. 255:167-171(1989).
CC -!- FUNCTION: Required for activation of most nif operons, which are
CC directly involved in nitrogen fixation.
CC -!- SUBUNIT: Interacts with sigma-54.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC47302.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAA29531.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X06167; CAA29532.1; -; Genomic_DNA.
DR EMBL; X06167; CAA29531.1; ALT_INIT; Genomic_DNA.
DR EMBL; BA000040; BAC47302.1; ALT_INIT; Genomic_DNA.
DR PIR; S01066; S01066.
DR RefSeq; NP_768677.1; NC_004463.1.
DR AlphaFoldDB; P05407; -.
DR SMR; P05407; -.
DR STRING; 224911.27350291; -.
DR EnsemblBacteria; BAC47302; BAC47302; BAC47302.
DR KEGG; bja:blr2037; -.
DR PATRIC; fig|224911.5.peg.1994; -.
DR eggNOG; COG3604; Bacteria.
DR HOGENOM; CLU_000445_95_2_5; -.
DR InParanoid; P05407; -.
DR OMA; NFQAKLL; -.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
DR GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
DR Gene3D; 3.30.450.40; -; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR003018; GAF.
DR InterPro; IPR029016; GAF-like_dom_sf.
DR InterPro; IPR002197; HTH_Fis.
DR InterPro; IPR010113; Nif-specific_regulatory_prot.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR002078; Sigma_54_int.
DR InterPro; IPR025662; Sigma_54_int_dom_ATP-bd_1.
DR InterPro; IPR025943; Sigma_54_int_dom_ATP-bd_2.
DR InterPro; IPR025944; Sigma_54_int_dom_CS.
DR Pfam; PF01590; GAF; 1.
DR Pfam; PF02954; HTH_8; 1.
DR Pfam; PF00158; Sigma54_activat; 1.
DR PRINTS; PR01590; HTHFIS.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00065; GAF; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01817; nifA; 1.
DR PROSITE; PS00675; SIGMA54_INTERACT_1; 1.
DR PROSITE; PS00676; SIGMA54_INTERACT_2; 1.
DR PROSITE; PS00688; SIGMA54_INTERACT_3; 1.
DR PROSITE; PS50045; SIGMA54_INTERACT_4; 1.
PE 1: Evidence at protein level;
KW Activator; ATP-binding; DNA-binding; Metal-binding; Nitrogen fixation;
KW Nucleotide-binding; Reference proteome; Transcription;
KW Transcription regulation; Two-component regulatory system.
FT CHAIN 1..582
FT /note="Nif-specific regulatory protein"
FT /id="PRO_0000081305"
FT DOMAIN 46..188
FT /note="GAF"
FT DOMAIN 230..458
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 554..573
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 459..539
FT /note="Inter-domain linker"
FT REGION 540..582
FT /note="C-terminal DNA-binding domain"
FT BINDING 258..265
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 321..330
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 472
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000305"
FT BINDING 477
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000305"
FT CONFLICT 223..224
FT /note="KQ -> NE (in Ref. 1; CAA29532/CAA29531)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 582 AA; 63098 MW; D3083178139EB812 CRC64;
MLHIPSSSER PASQPEPERA PPGEPSHESA LAGIYEISKI LNAPGRLEVT LANVLGLLQS
FVQMRHGLVS LFNDDGVPEL TVGAGWSEGT DERYRTCVPQ KAIHEIVATG RSLMVENVAA
ETAFSAADRE VLGASDSIPV AFIGVPIRVD STVVGTLTID RIPEGSSSLL EYDARLLAMV
ANVIGQTIKL HRLFAGDREQ SLVDKDRLEK QTVDRGPPAR ERKQLQAHGI IGDSPALSAL
LEKIVVVARS NSTVLLRGES GTGKELVAKA IHESSVRAKR PFVKLNCAAL PETVLESELF
GHEKGAFTGA VSARKGRFEL ADKGTLFLDE IGEISPPFQA KLLRVLQEQE FERVGSNHTI
KVDVRVIAAT NRNLEEAVAR SEFRADLYYR ISVVPLLLPP LRERRSDIPL LAREFLRKFN
SENGRSLTLE ASAIDVLMSC KFPGNVRELE NCIERTATLS AGTSIVRSDF ACSQGQCLST
TLWKSTSYGK TDPAAPMQPV PAKSIIPLAE TAPPPQAVCE PGSLAPSGTV LVSGARMADR
ERVVAAMEKS GWVQAKAARL LGLTPRQVGY ALRKYGIEIK RF
