DCTD_RHIME
ID DCTD_RHIME Reviewed; 460 AA.
AC P13632;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 24-OCT-2001, sequence version 3.
DT 03-AUG-2022, entry version 187.
DE RecName: Full=C4-dicarboxylate transport transcriptional regulatory protein DctD;
GN Name=dctD; OrderedLocusNames=RB1525; ORFNames=SMb20613;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OG Plasmid pSymB (megaplasmid 2).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=JJ1c10;
RX PubMed=2134335; DOI=10.1094/mpmi-3-174;
RA Watson R.J.;
RT "Analysis of the C4-dicarboxylate transport genes of Rhizobium meliloti:
RT nucleotide sequence and deduced products of dctA, dctB, and dctD.";
RL Mol. Plant Microbe Interact. 3:174-181(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=2793824; DOI=10.1128/jb.171.10.5244-5253.1989;
RA Jiang J., Gu B., Albright L.M., Nixon B.T.;
RT "Conservation between coding and regulatory elements of Rhizobium meliloti
RT and Rhizobium leguminosarum dct genes.";
RL J. Bacteriol. 171:5244-5253(1989).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481431; DOI=10.1073/pnas.161294698;
RA Finan T.M., Weidner S., Wong K., Buhrmester J., Chain P., Vorhoelter F.J.,
RA Hernandez-Lucas I., Becker A., Cowie A., Gouzy J., Golding B., Puehler A.;
RT "The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing
RT endosymbiont Sinorhizobium meliloti.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9889-9894(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 PHOSPHORYLATION.
RX PubMed=7896073; DOI=10.1111/j.1574-6968.1995.tb07385.x;
RA Giblin L., Boesten B., Turk S., Hooykaas P., O'Gara F.;
RT "Signal transduction in the Rhizobium meliloti dicarboxylic acid transport
RT system.";
RL FEMS Microbiol. Lett. 126:25-30(1995).
CC -!- FUNCTION: Member of the two-component regulatory system DctB/DctD
CC involved in the transport of C4-dicarboxylates. When activated by DctB
CC acts in conjunction with sigma-54 to activate the transcription of
CC dctA.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- PTM: Phosphorylated by DctB. {ECO:0000269|PubMed:7896073}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA63514.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; J03683; AAA63513.1; -; Genomic_DNA.
DR EMBL; J03683; AAA63514.1; ALT_INIT; Genomic_DNA.
DR EMBL; M26531; AAA26250.1; -; Genomic_DNA.
DR EMBL; AL591985; CAC49925.1; -; Genomic_DNA.
DR PIR; C33586; C33586.
DR PIR; E96032; E96032.
DR RefSeq; NP_438065.1; NC_003078.1.
DR RefSeq; WP_003529421.1; NC_003078.1.
DR PDB; 1L5Y; X-ray; 2.10 A; A/B=2-143.
DR PDB; 1L5Z; X-ray; 2.00 A; A=2-143.
DR PDB; 1QKK; X-ray; 1.70 A; A=2-143.
DR PDBsum; 1L5Y; -.
DR PDBsum; 1L5Z; -.
DR PDBsum; 1QKK; -.
DR AlphaFoldDB; P13632; -.
DR SMR; P13632; -.
DR MINT; P13632; -.
DR STRING; 266834.SM_b20613; -.
DR EnsemblBacteria; CAC49925; CAC49925; SM_b20613.
DR GeneID; 61601428; -.
DR KEGG; sme:SM_b20613; -.
DR PATRIC; fig|266834.11.peg.6450; -.
DR eggNOG; COG2204; Bacteria.
DR HOGENOM; CLU_000445_0_5_5; -.
DR OMA; DDQRNMR; -.
DR EvolutionaryTrace; P13632; -.
DR Proteomes; UP000001976; Plasmid pSymB.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
DR GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:InterPro.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011006; CheY-like_superfamily.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR002197; HTH_Fis.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
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; PF00072; Response_reg; 1.
DR Pfam; PF00158; Sigma54_activat; 1.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00448; REC; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR SUPFAM; SSF52172; SSF52172; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS50110; RESPONSE_REGULATORY; 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 1: Evidence at protein level;
KW 3D-structure; Activator; ATP-binding; Cytoplasm; DNA-binding;
KW Nucleotide-binding; Phosphoprotein; Plasmid; Reference proteome;
KW Transcription; Transcription regulation; Two-component regulatory system.
FT CHAIN 1..460
FT /note="C4-dicarboxylate transport transcriptional
FT regulatory protein DctD"
FT /id="PRO_0000081089"
FT DOMAIN 6..120
FT /note="Response regulatory"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00169"
FT DOMAIN 145..374
FT /note="Sigma-54 factor interaction"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT DNA_BIND 417..436
FT /note="H-T-H motif"
FT REGION 332..345
FT /note="Inter-domain linker"
FT /evidence="ECO:0000255"
FT BINDING 173..180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT BINDING 236..245
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00193"
FT MOD_RES 55
FT /note="4-aspartylphosphate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00169"
FT CONFLICT 43
FT /note="G -> E (in Ref. 1; AAA63513/AAA63514)"
FT /evidence="ECO:0000305"
FT CONFLICT 68
FT /note="R -> G (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 70
FT /note="I -> V (in Ref. 1)"
FT /evidence="ECO:0000305"
FT CONFLICT 151
FT /note="V -> A (in Ref. 1; AAA63513/AAA63514)"
FT /evidence="ECO:0000305"
FT STRAND 6..10
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 14..26
FT /evidence="ECO:0007829|PDB:1QKK"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 37..42
FT /evidence="ECO:0007829|PDB:1QKK"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1QKK"
FT STRAND 59..61
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:1QKK"
FT STRAND 79..83
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 85..87
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 88..96
FT /evidence="ECO:0007829|PDB:1QKK"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:1QKK"
FT HELIX 109..142
FT /evidence="ECO:0007829|PDB:1QKK"
SQ SEQUENCE 460 AA; 50061 MW; F6B9356EA089B38C CRC64;
MSAAPSVFLI DDDRDLRKAM QQTLELAGFT VSSFASATEA LAGLSADFAG IVISDIRMPG
MDGLALFRKI LALDPDLPMI LVTGHGDIPM AVQAIQDGAY DFIAKPFAAD RLVQSARRAE
EKRRLVMENR SLRRAAEAAS EGLPLIGQTP VMERLRQTLK HIADTDVDVL VAGETGSGKE
VVATLLHQWS RRRTGNFVAL NCGALPETVI ESELFGHEPG AFTGAVKKRI GRIEHASGGT
LFLDEIEAMP PATQVKMLRV LEAREITPLG TNLTRPVDIR VVAAAKVDLG DPAARGDFRE
DLYYRLNVVT LSIPPLRERR DDIPLLFSHF LARASERFGR EVPAISAAMR AYLATHSWPG
NVRELSHFAE RVALGVEGNL GVPAAAPASS GATLPERLER YEADILKQAL TAHCGDVKET
LQALGIPRKT FYDKLQRHGI NRADYVERAG PGRPNAISKT
