NIFA_AZOC5
ID NIFA_AZOC5 Reviewed; 615 AA.
AC P09133; A8HQP2;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-APR-1993, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Nif-specific regulatory protein;
GN Name=nifA; OrderedLocusNames=AZC_1049;
OS Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / LMG
OS 6465 / NBRC 14845 / NCIMB 13405 / ORS 571).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Xanthobacteraceae; Azorhizobium.
OX NCBI_TaxID=438753;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2664425; DOI=10.1111/j.1365-2958.1989.tb00231.x;
RA Ratet P., Pawlowski K., Schell J., de Bruijn F.J.;
RT "The Azorhizobium caulinodans nitrogen-fixation regulatory gene, nifA, is
RT controlled by the cellular nitrogen and oxygen status.";
RL Mol. Microbiol. 3:825-838(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3186446; DOI=10.1093/nar/16.20.9839;
RA Nees D.W., Stein P.A., Ludwig R.A.;
RT "The Azorhizobium caulinodans nifA gene: identification of upstream-
RT activating sequences including a new element, the 'anaerobox'.";
RL Nucleic Acids Res. 16:9839-9853(1988).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43989 / DSM 5975 / JCM 20966 / LMG 6465 / NBRC 14845 / NCIMB
RC 13405 / ORS 571;
RA Lee K.B., Backer P.D., Aono T., Liu C.T., Suzuki S., Suzuki T., Kaneko T.,
RA Yamada M., Tabata S., Kupfer D.M., Najar F.Z., Wiley G.B., Roe B.,
RA Binnewies T., Ussery D., Vereecke D., Gevers D., Holsters M., Oyaizu H.;
RT "Complete genome sequence of the nitrogen-fixing bacterium Azorhizobium
RT caulinodans ORS571.";
RL Submitted (APR-2007) 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.
CC -!- INDUCTION: NifA transcriptional activity seems to be controlled by both
CC the general nitrogen regulatory (ntr) system and the O(2)-regulatory
CC (FNR) system.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA30816.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC Sequence=CAA32837.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X14716; CAA32836.1; -; Genomic_DNA.
DR EMBL; X14716; CAA32837.1; ALT_INIT; Genomic_DNA.
DR EMBL; X08014; CAA30816.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP009384; BAF87047.1; -; Genomic_DNA.
DR PIR; S06977; S06977.
DR AlphaFoldDB; P09133; -.
DR SMR; P09133; -.
DR STRING; 438753.AZC_1049; -.
DR EnsemblBacteria; BAF87047; BAF87047; AZC_1049.
DR KEGG; azc:AZC_1049; -.
DR eggNOG; COG3604; Bacteria.
DR HOGENOM; CLU_000445_95_2_5; -.
DR OMA; RCKFPGN; -.
DR OrthoDB; 123059at2; -.
DR Proteomes; UP000000270; 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 2: Evidence at transcript 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..615
FT /note="Nif-specific regulatory protein"
FT /id="PRO_0000081301"
FT DOMAIN 68..210
FT /note="GAF"
FT DOMAIN 256..484
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 587..606
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 485..572
FT /note="Inter-domain linker"
FT REGION 573..615
FT /note="C-terminal DNA-binding domain"
FT BINDING 284..291
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 347..356
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 498
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P05407"
FT BINDING 503
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P05407"
SQ SEQUENCE 615 AA; 66794 MW; 3F1CF9D5F5A7B89E CRC64;
MPMTDAFQVR VPRVSSSTAG DIAASSITTR GALPRPGGMP VSMSRGTSPE VALIGVYEIS
KILTAPRRLE VTLANVVNVL SSMLQMRHGM ICILDSEGDP DMVATTGWTP EMAGQIRAHV
PQKAIDQIVA TQMPLVVQDV TADPLFAGHE DLFGPPEEAT VSFIGVPIKA DHHVMGTLSI
DRIWDGTARF RFDEDVRFLT MVANLVGQTV RLHKLVASDR DRLIAQTHRL EKALREEKSG
AEPEVAEAAN GSAMGIVGDS PLVKRLIATA QVVARSNSTV LLRGESGTGK ELFARAIHEL
SPRKGKPFVK VNCAALPESV LESELFGHEK GAFTGALNMR QGRFELAHGG TLFLDEIGEI
TPAFQAKLLR VLQEGEFERV GGNRTLKVDV RLVCATNKNL EEAVSKGEFR ADLYYRIHVV
PLILPPLRER PGDIPKLAKN FLDRFNKENK LHMMLSAPAI DVLRRCYFPG NVRELENCIR
RTATLAHDAV ITPHDFACDS GQCLSAMLWK GSAPKPVMPH VPPAPTPLTP LSPAPLATAA
PAAASPAPAA DSLPVTCPGT EACPAVPPRQ SEKEQLLQAM ERSGWVQAKA ARLLNLTPRQ
VGYALRKYDI DIKRF
