ID   NODD2_RHIME             Reviewed;         310 AA.
AC   P08719;
DT   01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT   24-OCT-2001, sequence version 2.
DT   25-MAY-2022, entry version 130.
DE   RecName: Full=Nodulation protein D 2;
GN   Name=nodD2; OrderedLocusNames=RA0404; ORFNames=SMa0757;
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=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   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=RCR2011 / SU47;
RX   PubMed=2298703; DOI=10.1128/jb.172.2.901-911.1990;
RA   Honma M.A., Asomaning M., Ausubel F.M.;
RT   "Rhizobium meliloti nodD genes mediate host-specific activation of
RT   nodABC.";
RL   J. Bacteriol. 172:901-911(1990).
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: 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.
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; X04474; CAA28162.1; -; Genomic_DNA.
DR   EMBL; M29367; AAA26336.1; -; Genomic_DNA.
DR   EMBL; AE006469; AAK65062.1; -; Genomic_DNA.
DR   PIR; B25788; B25788.
DR   PIR; D95312; D95312.
DR   RefSeq; NP_435650.1; NC_003037.1.
DR   RefSeq; WP_010967394.1; NC_003037.1.
DR   AlphaFoldDB; P08719; -.
DR   SMR; P08719; -.
DR   EnsemblBacteria; AAK65062; AAK65062; SMa0757.
DR   GeneID; 61599220; -.
DR   KEGG; sme:SMa0757; -.
DR   PATRIC; fig|266834.11.peg.422; -.
DR   HOGENOM; CLU_039613_39_0_5; -.
DR   OMA; CARPHVM; -.
DR   Proteomes; UP000001976; Plasmid pSymA.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
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..310
FT                   /note="Nodulation protein D 2"
FT                   /id="PRO_0000105719"
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"
FT   VARIANT         88
FT                   /note="D -> E (in strain: 41)"
FT   VARIANT         256
FT                   /note="T -> A (in strain: 41)"
FT   VARIANT         268
FT                   /note="P -> S (in strain: 41)"
SQ   SEQUENCE   310 AA;  35327 MW;  10EF405717C0B4D5 CRC64;
     MRFRGLDLNL LVALDALMTE RKLTAAARRV KLSQPAMSAA IARLRTYFGD ELFSMQGREL
     IPTPRAEALA PAVRDALLHI QLSVIAWDPI NPAQSDRRFR IILSDFMTLV FFERVVERLA
     REAPGVSFEL LPLDDDPYEL LRRGDVDFLV LPDLFMSSAH PKAKLFAEAL VCVGCPTNEQ
     LLGELSFEKY MSMGHVAAQF GRALKPSFEQ WLLLEHGFKR RVELVVPGFT LIPPLLPHTN
     RIAIIPLRLV KYFEQTIPLR IVKHPLPPLW FTEAVQWPAL HNKDPGNIWM REILLQEASR
     SEFQGETSLE