NIFA_RHIME
ID NIFA_RHIME Reviewed; 541 AA.
AC P03028;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 21-JUL-1986, sequence version 1.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=Nif-specific regulatory protein;
GN Name=nifA; Synonyms=fixD; OrderedLocusNames=RA0443; ORFNames=SMa0815;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OG Plasmid pSymA (megaplasmid 1).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2989799; DOI=10.1093/nar/13.12.4539;
RA Buikema W.J., Szeto W.W., Lemley P.V., Orme-Johnson W.H., Ausubel F.M.;
RT "Nitrogen fixation specific regulatory genes of Klebsiella pneumoniae and
RT Rhizobium meliloti share homology with the general nitrogen regulatory gene
RT ntrC of K. pneumoniae.";
RL Nucleic Acids Res. 13:4539-4555(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Weber G., Reilaender H., Puehler A.;
RT "Mapping and expression of a regulatory nitrogen fixation gene (fixD) of
RT Rhizobium meliloti.";
RL Submitted (FEB-1986) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481432; DOI=10.1073/pnas.161294798;
RA Barnett M.J., Fisher R.F., Jones T., Komp C., Abola A.P., Barloy-Hubler F.,
RA Bowser L., Capela D., Galibert F., Gouzy J., Gurjal M., Hong A., Huizar L.,
RA Hyman R.W., Kahn D., Kahn M.L., Kalman S., Keating D.H., Palm C.,
RA Peck M.C., Surzycki R., Wells D.H., Yeh K.-C., Davis R.W., Federspiel N.A.,
RA Long S.R.;
RT "Nucleotide sequence and predicted functions of the entire Sinorhizobium
RT meliloti pSymA megaplasmid.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9883-9888(2001).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
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=CAA26471.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X02615; CAA26470.1; -; Genomic_DNA.
DR EMBL; X02615; CAA26471.1; ALT_INIT; Genomic_DNA.
DR EMBL; X03065; CAA26869.1; -; Genomic_DNA.
DR EMBL; AE006469; AAK65101.2; -; Genomic_DNA.
DR PIR; A03563; RGZRAM.
DR PIR; C95317; C95317.
DR RefSeq; NP_435689.2; NC_003037.1.
DR RefSeq; WP_010967431.1; NC_003037.1.
DR AlphaFoldDB; P03028; -.
DR SMR; P03028; -.
DR PRIDE; P03028; -.
DR EnsemblBacteria; AAK65101; AAK65101; SMa0815.
DR GeneID; 61599254; -.
DR KEGG; sme:SMa0815; -.
DR PATRIC; fig|266834.11.peg.456; -.
DR HOGENOM; CLU_000445_95_2_5; -.
DR OMA; QAPIYIS; -.
DR Proteomes; UP000001976; Plasmid pSymA.
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; 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..541
FT /note="Nif-specific regulatory protein"
FT /id="PRO_0000081313"
FT DOMAIN 23..158
FT /note="GAF"
FT DOMAIN 200..428
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 513..532
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 170..191
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 429..498
FT /note="Inter-domain linker"
FT REGION 499..541
FT /note="C-terminal DNA-binding domain"
FT BINDING 228..235
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 291..300
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 442
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P05407"
FT BINDING 447
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P05407"
SQ SEQUENCE 541 AA; 59865 MW; BC82DD9710A98A02 CRC64;
MRKQDKRSAE IYSISKALMA PTRLETTLNN FVNTLSLILR MRRGGLEIPA SEGETKITAA
TRNSGSPSAA DYTVPKAAID QVMTAGRLVV PDVCNSELFK DQIKWRGIGP TAFIAAAVEV
DHETGGMLWF ECAEESDYDY EEEVHFLSMA ANLAGRAIRL HRTISRRERT FAEEQQEQQN
SRDEQSQSSA RQRLLKNDGI IGESTALMTA VDTAKVMAET NSIVLLRGET GTGKECFAKL
IHQHSTRQKK PFIKFNCPAL SESLLESELF GHEKGAFTGA IAQRVGRFES ANGGTLLLDE
IGEIPPAFQA KLLRVIQEGE FERVGGTKTL KVDVRLIFAT NKDLEMAVQN GEFREDLYYR
ISGVPLILPP LRHRDGDIPL LARAFLQRFN EENGRDLHFA PSALDHLSKC KFPGNVRELE
NCVRRTATLA RSKTITSSDF ACQTDQCFSS RLWKGVHCSH GHIEIDAPAG TTPLLGAPAN
DVPPKEPGSA GVASNLIERD RLISALEEAG WNQAKAARIL EKTPRQVGYA LRRHGVDVRK
L
