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Protein

C4-dicarboxylate transport transcriptional regulatory protein DctD

Gene

dctD

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi173 – 1808ATPPROSITE-ProRule annotation
Nucleotide bindingi236 – 24510ATPPROSITE-ProRule annotation
DNA bindingi417 – 43620H-T-H motifAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation, Two-component regulatory system

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-4958-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
C4-dicarboxylate transport transcriptional regulatory protein DctD
Gene namesi
Name:dctD
Ordered Locus Names:RB1525
ORF Names:SMb20613
Encoded oniPlasmid pSymB (megaplasmid 2)0 Publication
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 Componenti: Plasmid pSymB

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 460460C4-dicarboxylate transport transcriptional regulatory protein DctDPRO_0000081089Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei55 – 5514-aspartylphosphatePROSITE-ProRule annotation

Post-translational modificationi

Phosphorylated by DctB.1 Publication

Keywords - PTMi

Phosphoprotein

Interactioni

Protein-protein interaction databases

MINTiMINT-1506790.

Structurei

Secondary structure

1
460
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 105Combined sources
Helixi14 – 2613Combined sources
Beta strandi30 – 356Combined sources
Helixi37 – 426Combined sources
Beta strandi50 – 567Combined sources
Beta strandi59 – 613Combined sources
Helixi63 – 7311Combined sources
Beta strandi79 – 835Combined sources
Helixi85 – 873Combined sources
Helixi88 – 969Combined sources
Beta strandi101 – 1066Combined sources
Helixi109 – 14234Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L5YX-ray2.10A/B2-143[»]
1L5ZX-ray2.00A2-143[»]
1QKKX-ray1.70A2-143[»]
ProteinModelPortaliP13632.
SMRiP13632. Positions 5-143.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13632.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 120115Response regulatoryPROSITE-ProRule annotationAdd
BLAST
Domaini145 – 374230Sigma-54 factor interactionPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni332 – 34514Inter-domain linkerSequence analysisAdd
BLAST

Sequence similaritiesi

Contains 1 response regulatory domain.PROSITE-ProRule annotation
Contains 1 sigma-54 factor interaction domain.PROSITE-ProRule annotation

Phylogenomic databases

KOiK10126.
OMAiHIVEINQ.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR011006. CheY-like_superfamily.
IPR009057. Homeodomain-like.
IPR002197. HTH_Fis.
IPR027417. P-loop_NTPase.
IPR001789. Sig_transdc_resp-reg_receiver.
IPR002078. Sigma_54_int.
IPR025662. Sigma_54_int_dom_ATP-bd_1.
IPR025943. Sigma_54_int_dom_ATP-bd_2.
IPR025944. Sigma_54_int_dom_CS.
[Graphical view]
PfamiPF02954. HTH_8. 1 hit.
PF00072. Response_reg. 1 hit.
PF00158. Sigma54_activat. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00448. REC. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF52172. SSF52172. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50110. RESPONSE_REGULATORY. 1 hit.
PS00675. SIGMA54_INTERACT_1. 1 hit.
PS00676. SIGMA54_INTERACT_2. 1 hit.
PS00688. SIGMA54_INTERACT_3. 1 hit.
PS50045. SIGMA54_INTERACT_4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P13632-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAAPSVFLI DDDRDLRKAM QQTLELAGFT VSSFASATEA LAGLSADFAG
60 70 80 90 100
IVISDIRMPG MDGLALFRKI LALDPDLPMI LVTGHGDIPM AVQAIQDGAY
110 120 130 140 150
DFIAKPFAAD RLVQSARRAE EKRRLVMENR SLRRAAEAAS EGLPLIGQTP
160 170 180 190 200
VMERLRQTLK HIADTDVDVL VAGETGSGKE VVATLLHQWS RRRTGNFVAL
210 220 230 240 250
NCGALPETVI ESELFGHEPG AFTGAVKKRI GRIEHASGGT LFLDEIEAMP
260 270 280 290 300
PATQVKMLRV LEAREITPLG TNLTRPVDIR VVAAAKVDLG DPAARGDFRE
310 320 330 340 350
DLYYRLNVVT LSIPPLRERR DDIPLLFSHF LARASERFGR EVPAISAAMR
360 370 380 390 400
AYLATHSWPG NVRELSHFAE RVALGVEGNL GVPAAAPASS GATLPERLER
410 420 430 440 450
YEADILKQAL TAHCGDVKET LQALGIPRKT FYDKLQRHGI NRADYVERAG
460
PGRPNAISKT
Length:460
Mass (Da):50,061
Last modified:October 24, 2001 - v3
Checksum:iF6B9356EA089B38C
GO

Sequence cautioni

The sequence AAA63514 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti43 – 431G → E in AAA63513 (PubMed:2134335).Curated
Sequence conflicti43 – 431G → E in AAA63514 (PubMed:2134335).Curated
Sequence conflicti68 – 681R → G (PubMed:2134335).Curated
Sequence conflicti70 – 701I → V (PubMed:2134335).Curated
Sequence conflicti151 – 1511V → A in AAA63513 (PubMed:2134335).Curated
Sequence conflicti151 – 1511V → A in AAA63514 (PubMed:2134335).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03683 Genomic DNA. Translation: AAA63513.1.
J03683 Genomic DNA. Translation: AAA63514.1. Different initiation.
M26531 Genomic DNA. Translation: AAA26250.1.
AL591985 Genomic DNA. Translation: CAC49925.1.
PIRiC33586.
E96032.
RefSeqiNP_438065.1. NC_003078.1.
WP_003529421.1. NC_003078.1.

Genome annotation databases

EnsemblBacteriaiCAC49925; CAC49925; SM_b20613.
GeneIDi1237857.
KEGGisme:SM_b20613.
PATRICi23639460. VBISinMel96828_6450.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J03683 Genomic DNA. Translation: AAA63513.1.
J03683 Genomic DNA. Translation: AAA63514.1. Different initiation.
M26531 Genomic DNA. Translation: AAA26250.1.
AL591985 Genomic DNA. Translation: CAC49925.1.
PIRiC33586.
E96032.
RefSeqiNP_438065.1. NC_003078.1.
WP_003529421.1. NC_003078.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1L5YX-ray2.10A/B2-143[»]
1L5ZX-ray2.00A2-143[»]
1QKKX-ray1.70A2-143[»]
ProteinModelPortaliP13632.
SMRiP13632. Positions 5-143.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-1506790.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC49925; CAC49925; SM_b20613.
GeneIDi1237857.
KEGGisme:SM_b20613.
PATRICi23639460. VBISinMel96828_6450.

Phylogenomic databases

KOiK10126.
OMAiHIVEINQ.

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-4958-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP13632.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR011006. CheY-like_superfamily.
IPR009057. Homeodomain-like.
IPR002197. HTH_Fis.
IPR027417. P-loop_NTPase.
IPR001789. Sig_transdc_resp-reg_receiver.
IPR002078. Sigma_54_int.
IPR025662. Sigma_54_int_dom_ATP-bd_1.
IPR025943. Sigma_54_int_dom_ATP-bd_2.
IPR025944. Sigma_54_int_dom_CS.
[Graphical view]
PfamiPF02954. HTH_8. 1 hit.
PF00072. Response_reg. 1 hit.
PF00158. Sigma54_activat. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00448. REC. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF52172. SSF52172. 1 hit.
SSF52540. SSF52540. 1 hit.
PROSITEiPS50110. RESPONSE_REGULATORY. 1 hit.
PS00675. SIGMA54_INTERACT_1. 1 hit.
PS00676. SIGMA54_INTERACT_2. 1 hit.
PS00688. SIGMA54_INTERACT_3. 1 hit.
PS50045. SIGMA54_INTERACT_4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDCTD_RHIME
AccessioniPrimary (citable) accession number: P13632
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: October 24, 2001
Last modified: September 7, 2016
This is version 156 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Plasmid, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.