NODD1_RHIME
ID NODD1_RHIME Reviewed; 308 AA.
AC P03031;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1988, sequence version 1.
DT 25-MAY-2022, entry version 134.
DE RecName: Full=Nodulation protein D 1;
GN Name=nodD1; OrderedLocusNames=RA0476; ORFNames=SMa0870;
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].
RC STRAIN=1021;
RX PubMed=4006668; DOI=10.1089/dna.1985.4.241;
RA Egelhoff T.T., Fisher R.F., Jacobs T.W., Mulligan J.T., Long S.R.;
RT "Nucleotide sequence of Rhizobium meliloti 1021 nodulation genes: nodD is
RT read divergently from nodABC.";
RL DNA 4:241-248(1985).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=41;
RX PubMed=3820290; DOI=10.1016/0022-2836(86)90136-1;
RA Goettfert M., Horvath B., Kondorosi E., Putnoky P., Rodriguez-Quinones F.,
RA Kondorosi A.;
RT "At least two nodD genes are necessary for efficient nodulation of alfalfa
RT by Rhizobium meliloti.";
RL J. Mol. Biol. 191:411-420(1986).
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).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-5.
RC STRAIN=41;
RX PubMed=6336331; DOI=10.1093/nar/12.24.9509;
RA Toeroek I., Kondorosi E., Stepkowski T., Posfai J., Kondorosi A.;
RT "Nucleotide sequence of Rhizobium meliloti nodulation genes.";
RL Nucleic Acids Res. 12:9509-9524(1984).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 88-308.
RX PubMed=3316182; DOI=10.1128/jb.169.12.5393-5400.1987;
RA Aguilar O.M., Reilaender H., Arnold W., Puehler A.;
RT "Rhizobium meliloti nifN (fixF) gene is part of an operon regulated by a
RT nifA-dependent promoter and codes for a polypeptide homologous to the nifK
RT gene product.";
RL J. Bacteriol. 169:5393-5400(1987).
RN [7]
RP FUNCTIONAL REGIONS.
RA Spaink H.P., Wijffelman C.A., Okker R.J.H., Lugtenberg B.E.J.;
RT "Localization of functional regions of the Rhizobium nodD product using
RT hybrid nodD genes.";
RL Plant Mol. Biol. 12:59-73(1989).
CC -!- FUNCTION: NodD regulates the expression of the nodABCFE genes which
CC encode other nodulation proteins. NodD is also a negative regulator of
CC its own expression. Binds flavonoids as inducers. {ECO:0000269|Ref.7}.
CC -!- MISCELLANEOUS: There are at least three nodD genes in R.meliloti. They
CC differ in their specificity of interaction with different flavonoids
CC and, consequently, contribute to the nodulation of various plant host
CC species to different extents.
CC -!- SIMILARITY: Belongs to the LysR transcriptional regulatory family.
CC {ECO:0000305}.
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DR EMBL; M11268; AAA98359.1; -; Genomic_DNA.
DR EMBL; X04473; CAA28161.1; -; Genomic_DNA.
DR EMBL; AE006469; AAK65134.1; -; Genomic_DNA.
DR EMBL; M18272; AAA88518.1; -; Genomic_DNA.
DR PIR; A03566; ZZZRDM.
DR PIR; D95321; D95321.
DR RefSeq; NP_435722.1; NC_003037.1.
DR RefSeq; WP_010967456.1; NC_003037.1.
DR AlphaFoldDB; P03031; -.
DR SMR; P03031; -.
DR EnsemblBacteria; AAK65134; AAK65134; SMa0870.
DR GeneID; 25011497; -.
DR GeneID; 61599278; -.
DR KEGG; sme:SMa0870; -.
DR PATRIC; fig|266834.11.peg.487; -.
DR HOGENOM; CLU_039613_39_0_5; -.
DR OMA; DVDFLIF; -.
DR PRO; PR:P03031; -.
DR Proteomes; UP000001976; Plasmid pSymA.
DR CollecTF; EXPREG_000006d0; -.
DR GO; GO:0032993; C:protein-DNA complex; IPI:CollecTF.
DR GO; GO:0001216; F:DNA-binding transcription activator activity; IPI:CollecTF.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:CollecTF.
DR CDD; cd08462; PBP2_NodD; 1.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR005119; LysR_subst-bd.
DR InterPro; IPR037416; NodD_PBP2.
DR InterPro; IPR000847; Tscrpt_reg_HTH_LysR.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR InterPro; IPR036390; WH_DNA-bd_sf.
DR Pfam; PF00126; HTH_1; 1.
DR Pfam; PF03466; LysR_substrate; 1.
DR PRINTS; PR00039; HTHLYSR.
DR SUPFAM; SSF46785; SSF46785; 1.
DR PROSITE; PS50931; HTH_LYSR; 1.
PE 3: Inferred from homology;
KW Activator; DNA-binding; Nodulation; Plasmid; Reference proteome; Repressor;
KW Transcription; Transcription regulation.
FT CHAIN 1..308
FT /note="Nodulation protein D 1"
FT /id="PRO_0000105718"
FT DOMAIN 6..63
FT /note="HTH lysR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00253"
FT DNA_BIND 23..42
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00253"
SQ SEQUENCE 308 AA; 34880 MW; A8C1A5A45B452CC5 CRC64;
MRFRGLDLNL LVALDALMTE RKLTAAARRI NLSQPAMSAA IARLRTYFGD ELFSMQGREL
IPTPRAEALA PAVRDALLHI QLSVIAWDPL NPAQSDRRFR IILSDFMILV FFARIVERVA
REAPGVSFEL LPLDDDPHEL LRRGDVDFLI FPDVFMSSAH PKAKLFDEAL VCVGCPTNKK
LLGNISFETY MSMGHVAAQF GREMKPSVEQ WLLLEHGFNR RIELVVPGFT LIPRLLSGTN
RIATLPLRLV KYFEQTIPLR IVTSPLPPLF FTEAIQWPAL HNTDPGNIWL REILLQEASR
IDPQSDTC
