NODD3_RHIME
ID NODD3_RHIME Reviewed; 313 AA.
AC P23190;
DT 01-NOV-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1991, sequence version 1.
DT 25-MAY-2022, entry version 127.
DE RecName: Full=Nodulation protein D 3;
GN Name=nodD3; OrderedLocusNames=RA0458; ORFNames=SMa0840;
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=RCR2011 / SU47;
RX PubMed=2017373; DOI=10.1093/nar/19.4.921;
RA Rushing B.G., Yelton M.M., Long S.R.;
RT "Genetic and physical analysis of the nodD3 region of Rhizobium meliloti.";
RL Nucleic Acids Res. 19:921-927(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=AK631;
RX PubMed=1809842; DOI=10.1111/j.1365-2958.1991.tb01863.x;
RA Kondorosi E., Buire M., Cren M., Iyer N., Hoffmann B., Kondorosi A.;
RT "Involvement of the syrM and nodD3 genes of Rhizobium meliloti in nod gene
RT activation and in optimal nodulation of the plant host.";
RL Mol. Microbiol. 5:3035-3048(1991).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA43697.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; X53820; CAA37817.1; -; Genomic_DNA.
DR EMBL; X61457; CAA43697.1; ALT_INIT; Genomic_DNA.
DR EMBL; AE006469; AAK65116.1; -; Genomic_DNA.
DR PIR; B95319; B95319.
DR PIR; S26838; S26838.
DR RefSeq; NP_435704.1; NC_003037.1.
DR RefSeq; WP_010967440.1; NC_003037.1.
DR AlphaFoldDB; P23190; -.
DR SMR; P23190; -.
DR DNASU; 1235494; -.
DR EnsemblBacteria; AAK65116; AAK65116; SMa0840.
DR GeneID; 61599265; -.
DR KEGG; sme:SMa0840; -.
DR PATRIC; fig|266834.11.peg.469; -.
DR HOGENOM; CLU_039613_39_0_5; -.
DR OMA; CVMRQGH; -.
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; 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 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..313
FT /note="Nodulation protein D 3"
FT /id="PRO_0000105720"
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 CONFLICT 232
FT /note="I -> V (in Ref. 2; CAA43697)"
FT /evidence="ECO:0000305"
FT CONFLICT 256
FT /note="S -> N (in Ref. 2; CAA43697)"
FT /evidence="ECO:0000305"
FT CONFLICT 310..313
FT /note="CLGR -> VLGVRH (in Ref. 2)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 313 AA; 35342 MW; 1B1B3431AA07E5E7 CRC64;
MRFKGLDLNL LVALDALMTK RSVTAAARSI NLSQPAMSSA IARLRSYFQD ELFRMQGREL
ITTPRAEALA PAIRDALLHI QFSIISWDMF NPAQSDRCFR IILSDFMTLV FFEKVVERVA
REAPGVSFEL LPPDDNPDEL LRRGEVDFLI FPDVFMSSVH PKAKLFDQTL VSVGCLTNEQ
LLGDLSFERY MSMGHVAAQF GRALKPSVEQ WLLLEHGYKR RIELVVPGFN LIPPLLSGTK
RIAIIPLRLA NHFAKSIPLR IVKHPLPLLS FTEAVQWPAL HNKDQASIWM REILLDEAAR
IAAPRETAGC LGR
