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C4-dicarboxylate transport transcriptional regulatory protein DctD

 DCTD_RHIME              Reviewed;         460 AA.
P13632;
01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
24-OCT-2001, sequence version 3.
22-NOV-2017, entry version 167.
RecName: Full=C4-dicarboxylate transport transcriptional regulatory protein DctD;
Name=dctD; OrderedLocusNames=RB1525; ORFNames=SMb20613;
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
meliloti).
Plasmid pSymB (megaplasmid 2).
Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
NCBI_TaxID=266834;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=JJ1c10;
PubMed=2134335;
Watson R.J.;
"Analysis of the C4-dicarboxylate transport genes of Rhizobium
meliloti: nucleotide sequence and deduced products of dctA, dctB, and
dctD.";
Mol. Plant Microbe Interact. 3:174-181(1990).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=1021;
PubMed=2793824; DOI=10.1128/jb.171.10.5244-5253.1989;
Jiang J., Gu B., Albright L.M., Nixon B.T.;
"Conservation between coding and regulatory elements of Rhizobium
meliloti and Rhizobium leguminosarum dct genes.";
J. Bacteriol. 171:5244-5253(1989).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=1021;
PubMed=11481431; DOI=10.1073/pnas.161294698;
Finan T.M., Weidner S., Wong K., Buhrmester J., Chain P.,
Vorhoelter F.J., Hernandez-Lucas I., Becker A., Cowie A., Gouzy J.,
Golding B., Puehler A.;
"The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-
fixing endosymbiont Sinorhizobium meliloti.";
Proc. Natl. Acad. Sci. U.S.A. 98:9889-9894(2001).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=1021;
PubMed=11474104; DOI=10.1126/science.1060966;
Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F.,
Gloux S., Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M.,
Hernandez-Lucas I., Hong A., Huizar L., Hyman R.W., Jones T., Kahn D.,
Kahn M.L., Kalman S., Keating D.H., Kiss E., Komp C., Lelaure V.,
Masuy D., Palm C., Peck M.C., Pohl T.M., Portetelle D., Purnelle B.,
Ramsperger U., Surzycki R., Thebault P., Vandenbol M.,
Vorhoelter F.J., Weidner S., Wells D.H., Wong K., Yeh K.-C., Batut J.;
"The composite genome of the legume symbiont Sinorhizobium meliloti.";
Science 293:668-672(2001).
[5]
PHOSPHORYLATION.
PubMed=7896073; DOI=10.1111/j.1574-6968.1995.tb07385.x;
Giblin L., Boesten B., Turk S., Hooykaas P., O'Gara F.;
"Signal transduction in the Rhizobium meliloti dicarboxylic acid
transport system.";
FEMS Microbiol. Lett. 126:25-30(1995).
-!- FUNCTION: Member of the two-component regulatory system DctB/DctD
involved in the transport of C4-dicarboxylates. When activated by
DctB acts in conjunction with sigma-54 to activate the
transcription of dctA.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- PTM: Phosphorylated by DctB. {ECO:0000269|PubMed:7896073}.
-!- SEQUENCE CAUTION:
Sequence=AAA63514.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; J03683; AAA63513.1; -; Genomic_DNA.
EMBL; J03683; AAA63514.1; ALT_INIT; Genomic_DNA.
EMBL; M26531; AAA26250.1; -; Genomic_DNA.
EMBL; AL591985; CAC49925.1; -; Genomic_DNA.
PIR; C33586; C33586.
PIR; E96032; E96032.
RefSeq; NP_438065.1; NC_003078.1.
RefSeq; WP_003529421.1; NC_003078.1.
PDB; 1L5Y; X-ray; 2.10 A; A/B=2-143.
PDB; 1L5Z; X-ray; 2.00 A; A=2-143.
PDB; 1QKK; X-ray; 1.70 A; A=2-143.
PDBsum; 1L5Y; -.
PDBsum; 1L5Z; -.
PDBsum; 1QKK; -.
ProteinModelPortal; P13632; -.
SMR; P13632; -.
MINT; MINT-1506790; -.
DrugBank; DB04077; Glycerol.
EnsemblBacteria; CAC49925; CAC49925; SM_b20613.
GeneID; 1237857; -.
KEGG; sme:SM_b20613; -.
PATRIC; fig|266834.11.peg.6450; -.
KO; K10126; -.
OMA; MPISMQV; -.
EvolutionaryTrace; P13632; -.
Proteomes; UP000001976; Plasmid pSymB.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0043565; F:sequence-specific DNA binding; IEA:InterPro.
GO; GO:0008134; F:transcription factor binding; IEA:InterPro.
GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00156; REC; 1.
InterPro; IPR003593; AAA+_ATPase.
InterPro; IPR011006; CheY-like_superfamily.
InterPro; IPR009057; Homeobox-like_sf.
InterPro; IPR002197; HTH_Fis.
InterPro; IPR027417; P-loop_NTPase.
InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
InterPro; IPR002078; Sigma_54_int.
InterPro; IPR025662; Sigma_54_int_dom_ATP-bd_1.
InterPro; IPR025943; Sigma_54_int_dom_ATP-bd_2.
InterPro; IPR025944; Sigma_54_int_dom_CS.
Pfam; PF02954; HTH_8; 1.
Pfam; PF00072; Response_reg; 1.
Pfam; PF00158; Sigma54_activat; 1.
SMART; SM00382; AAA; 1.
SMART; SM00448; REC; 1.
SUPFAM; SSF46689; SSF46689; 1.
SUPFAM; SSF52172; SSF52172; 1.
SUPFAM; SSF52540; SSF52540; 1.
PROSITE; PS50110; RESPONSE_REGULATORY; 1.
PROSITE; PS00675; SIGMA54_INTERACT_1; 1.
PROSITE; PS00676; SIGMA54_INTERACT_2; 1.
PROSITE; PS00688; SIGMA54_INTERACT_3; 1.
PROSITE; PS50045; SIGMA54_INTERACT_4; 1.
1: Evidence at protein level;
3D-structure; Activator; ATP-binding; Complete proteome; Cytoplasm;
DNA-binding; Nucleotide-binding; Phosphoprotein; Plasmid;
Reference proteome; Transcription; Transcription regulation;
Two-component regulatory system.
CHAIN 1 460 C4-dicarboxylate transport
transcriptional regulatory protein DctD.
/FTId=PRO_0000081089.
DOMAIN 6 120 Response regulatory.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
DOMAIN 145 374 Sigma-54 factor interaction.
{ECO:0000255|PROSITE-ProRule:PRU00193}.
NP_BIND 173 180 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00193}.
NP_BIND 236 245 ATP. {ECO:0000255|PROSITE-
ProRule:PRU00193}.
DNA_BIND 417 436 H-T-H motif.
REGION 332 345 Inter-domain linker. {ECO:0000255}.
MOD_RES 55 55 4-aspartylphosphate.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
CONFLICT 43 43 G -> E (in Ref. 1; AAA63513/AAA63514).
{ECO:0000305}.
CONFLICT 68 68 R -> G (in Ref. 1). {ECO:0000305}.
CONFLICT 70 70 I -> V (in Ref. 1). {ECO:0000305}.
CONFLICT 151 151 V -> A (in Ref. 1; AAA63513/AAA63514).
{ECO:0000305}.
STRAND 6 10 {ECO:0000244|PDB:1QKK}.
HELIX 14 26 {ECO:0000244|PDB:1QKK}.
STRAND 30 35 {ECO:0000244|PDB:1QKK}.
HELIX 37 42 {ECO:0000244|PDB:1QKK}.
STRAND 50 56 {ECO:0000244|PDB:1QKK}.
STRAND 59 61 {ECO:0000244|PDB:1QKK}.
HELIX 63 73 {ECO:0000244|PDB:1QKK}.
STRAND 79 83 {ECO:0000244|PDB:1QKK}.
HELIX 85 87 {ECO:0000244|PDB:1QKK}.
HELIX 88 96 {ECO:0000244|PDB:1QKK}.
STRAND 101 106 {ECO:0000244|PDB:1QKK}.
HELIX 109 142 {ECO:0000244|PDB:1QKK}.
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


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