ID   NIFA_RHOCA              Reviewed;         579 AA.
AC   P0CY94; P09434; Q8RU04;
DT   28-JUN-2011, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   03-AUG-2022, entry version 44.
DE   RecName: Full=Nif-specific regulatory protein;
GN   Name=nifA1; Synonyms=nifA;
OS   Rhodobacter capsulatus (Rhodopseudomonas capsulata).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Rhodobacteraceae; Rhodobacter.
OX   NCBI_TaxID=1061;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=2836706; DOI=10.1007/bf00322441;
RA   Masepohl P., Klipp W., Puehler A.;
RT   "Genetic characterization and sequence analysis of the duplicated nifA/nifB
RT   gene region of Rhodobacter capsulatus.";
RL   Mol. Gen. Genet. 212:27-37(1988).
RN   [2]
RP   SEQUENCE REVISION TO N-TERMINUS.
RA   Masepohl P., Klipp W., Puehler A.;
RL   Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Required for activation of most nif operons, which are
CC       directly involved in nitrogen fixation.
CC   -!- SUBUNIT: Interacts with sigma-54.
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DR   EMBL; X07567; CAB53157.1; -; Genomic_DNA.
DR   PIR; S03828; S03828.
DR   AlphaFoldDB; P0CY94; -.
DR   SMR; P0CY94; -.
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; IPR009057; Homeobox-like_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; PF13185; GAF_2; 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; SSF46689; SSF46689; 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   4: Predicted;
KW   Activator; ATP-binding; DNA-binding; Metal-binding; Nitrogen fixation;
KW   Nucleotide-binding; Repeat; Transcription; Transcription regulation;
KW   Two-component regulatory system.
FT   CHAIN           1..579
FT                   /note="Nif-specific regulatory protein"
FT                   /id="PRO_0000081315"
FT   DOMAIN          40..187
FT                   /note="GAF"
FT   DOMAIN          226..454
FT                   /note="Sigma-54 factor interaction"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   REPEAT          505..506
FT                   /note="1"
FT   REPEAT          507..508
FT                   /note="2"
FT   REPEAT          509..510
FT                   /note="3"
FT   REPEAT          511..512
FT                   /note="4"
FT   REPEAT          513..514
FT                   /note="5"
FT   REPEAT          515..516
FT                   /note="6"
FT   REPEAT          517..518
FT                   /note="7"
FT   DNA_BIND        551..570
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000250"
FT   REGION          464..536
FT                   /note="Inter-domain linker"
FT   REGION          502..529
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          505..518
FT                   /note="7 X 2 AA tandem repeats of X-P"
FT   REGION          537..579
FT                   /note="C-terminal DNA-binding domain"
FT   COMPBIAS        503..521
FT                   /note="Pro residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         254..261
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         317..326
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         468
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
FT   BINDING         473
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
SQ   SEQUENCE   579 AA;  62926 MW;  FBABC1C5C4E2CB8D CRC64;
     MTDQQSRPAS PRRRSTQSIA DRLALDALYE IAKTFAAAPD PVAEVPQIFN VLSSFLDLRH
     GVLALLAEPG EGAGVNPYVI AATAFQRSPE APAADVLPDA VARIVFRSGV PFVSFDLVAE
     FGAEAVPKRL RDAGQTLIAV PLRDPERSHF VLGVLAAYRS HDHNRSGFSD ADVRVLTMVA
     SLLEQALRFR RRIARDRERA LEDTRRMLQT VTEQRGPAAP VSLDGIVGSS PAIAEVVAQI
     KRVASTRMPV LLRGESGTGK ELFARAVHAQ SPRAKGPFIR VNCAALSETL LESELFGHEK
     GAFTGATALK KGRFELADGG TLFLDEIGEI SPAFQSKLLR VLQEGEFERV GGAKTIKVDT
     RIVAATNRDL EDAVARGQFR ADLYFRICVV PIVLPPLRNR KSDIKPLAQL FLDRFNKQNA
     TNVKFAADAF DQICRCQFPG NVRELENCVN RAAALSDGAI VLAEELACRQ GACLSAELFR
     LQDGTSPIGG LAVGRVITPT VRVSAPPPEP APAPEPAPEA PPREEVPLRT KTAQLSREEL
     LRALESAGWV QAKAARLLGM TPRQIAYALQ KFEIELRKI