ID   NIFA_RHIEC              Reviewed;         584 AA.
AC   P54931; Q79BF1;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-1996, sequence version 1.
DT   03-AUG-2022, entry version 148.
DE   RecName: Full=Nif-specific regulatory protein;
GN   Name=nifA; OrderedLocusNames=RHE_PD00228;
OS   Rhizobium etli (strain CFN 42 / ATCC 51251).
OG   Plasmid sym p42d.
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX   NCBI_TaxID=347834;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Girard L., Valderrama B., Palacios R., Romero D., Devila G.;
RT   "Global transcriptional patterns in the symbiotic plasmid of Rhizobium etli
RT   CFN42.";
RL   Submitted (JAN-1996) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CFN 42 / ATCC 51251;
RX   PubMed=12801410; DOI=10.1186/gb-2003-4-6-r36;
RA   Gonzalez V., Bustos P., Ramirez-Romero M.A., Medrano-Soto A., Salgado H.,
RA   Hernandez-Gonzalez I., Hernandez-Celis J.C., Quintero V.,
RA   Moreno-Hagelsieb G., Girard L., Rodriguez O., Flores M., Cevallos M.A.,
RA   Collado-Vides J., Romero D., Davila G.;
RT   "The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and
RT   its relation to other symbiotic genome compartments.";
RL   Genome Biol. 4:R36.1-R36.13(2003).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CFN 42 / ATCC 51251;
RX   PubMed=16505379; DOI=10.1073/pnas.0508502103;
RA   Gonzalez V., Santamaria R.I., Bustos P., Hernandez-Gonzalez I.,
RA   Medrano-Soto A., Moreno-Hagelsieb G., Janga S.C., Ramirez M.A.,
RA   Jimenez-Jacinto V., Collado-Vides J., Davila G.;
RT   "The partitioned Rhizobium etli genome: genetic and metabolic redundancy in
RT   seven interacting replicons.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:3834-3839(2006).
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=AAM54823.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; U31630; AAA84917.1; -; Genomic_DNA.
DR   EMBL; U80928; AAM54823.2; ALT_INIT; Genomic_DNA.
DR   AlphaFoldDB; P54931; -.
DR   SMR; P54931; -.
DR   PRIDE; P54931; -.
DR   EnsemblBacteria; AAM54823; AAM54823; RHE_PD00228.
DR   KEGG; ret:RHE_PD00228; -.
DR   HOGENOM; CLU_000445_95_2_5; -.
DR   Proteomes; UP000001936; Plasmid sym p42d.
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   4: Predicted;
KW   Activator; ATP-binding; DNA-binding; Metal-binding; Nitrogen fixation;
KW   Nucleotide-binding; Plasmid; Reference proteome; Transcription;
KW   Transcription regulation; Two-component regulatory system.
FT   CHAIN           1..584
FT                   /note="Nif-specific regulatory protein"
FT                   /id="PRO_0000081310"
FT   DOMAIN          45..187
FT                   /note="GAF"
FT   DOMAIN          229..457
FT                   /note="Sigma-54 factor interaction"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   DNA_BIND        556..575
FT                   /note="H-T-H motif"
FT                   /evidence="ECO:0000250"
FT   REGION          1..24
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          458..541
FT                   /note="Inter-domain linker"
FT   REGION          495..518
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          542..584
FT                   /note="C-terminal DNA-binding domain"
FT   COMPBIAS        498..516
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         257..264
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         320..329
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT   BINDING         471
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
FT   BINDING         476
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000250|UniProtKB:P05407"
SQ   SEQUENCE   584 AA;  62898 MW;  7A84B361E322E2AA CRC64;
     MTHMPARPVD GAEPLSALPA GPMRQAGTQR SGIYEISKVL TAPARLEITL ANVVNVLSSF
     LQIRCGAIVV LDAEGQPEIA ATGDIPPSSQ SAARGVIPKA VIDHIATTGM PLIVKDVSKS
     ELFQAEPQPP WSSGTVPISF IGVPVKADNK ILGTISIDRV RNDAAPFPAD EDVRFLTMVA
     NLVSRTIRLH RFLNLEGRRP IGEQERPEKP IIAQRGAPGR HPPVKIDGII GDSPALQQVV
     ETVSVVARTN STVLLRGESG TGKEFFAQAI HELSPRKNKP FVKLNCAALP EGVLESELFG
     HEKGAFTGAI AQRAGRFELA NGGTLLLDEI GEISPAFQAK LLRVLQEGEL ERVGGTKTLA
     VDVRLICATN KNLEMAVANA EFRADLYYRI SVVPIVLPPL RERPGDIPRL ANALLDRFNK
     ENQRELTFSS SAIEVMSQCY FPGNVRELEN CVRRTATLAR SSSIVSSDFA CKNSQCLSSL
     LWKTDGSPGG ITVDGHARSN VMPTSSPRSG GSIGASDEVS SVKACDPHGS GCPAMESRLT
     QRDRLIEAME KAGWVQAKAA RILGLTPRQV GYALRQHRIE VKKL