ttdR:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

TtdR

Synonyms

predicted DNA-binding transcriptional regulator[1], TtdR[2][1], B3060[2][1], YgiP[2][1] , dan, ECK3050, JW3032, ygiP, b3060

Product description

predicted DNA-binding transcriptional regulator LYSR-type[2][3]

Transcriptional activator of ttdAB-ygjE, tartrate-inducible; required for tartrate utilization [4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003700

transcription factor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

sequence-specific DNA binding transcription factor activity

PMID:16804186[6]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0003700

transcription factor activity

PMID:19661178[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0001216

DNA-binding transcription activator activity

PMID:16804186[6]

IMP: Inferred from Mutant Phenotype

F

complete

GO:0001216

DNA-binding transcription activator activity

PMID:19661178[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0045893

positive regulation of transcription, DNA-templated

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030


P

Seeded from EcoCyc (v14.0)

complete

GO:0045893

positive regulation of transcription, DNA-templated

PMID:16804186[6]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0045893

positive regulation of transcription, DNA-templated

PMID:19661178[7]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

lsrF

PMID:16606699[8]

Experiment(s):EBI-1144678

Protein

groL

PMID:16606699[8]

Experiment(s):EBI-1144678
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MLNSWPLAKD LQVLVEIVHS GSFSAAAATL GQTPAFVTKR IQILENTLAT TLLNRSARGV
ALTESGQRCY EHALEILTQY QRLVDDVTQI KTRPEGMIRI GCSFGFGRSH IAPAITELMR
NYPELQVHFE LFDRQIDLVQ DNIDLDIRIN DEIPDYYIAH LLTKNKRILC AAPEYLQKYP
QPQSLQELSR HDCLVTKERD MTHGIWELGN GQEKKSVKVS GHLSSNSGEI VLQWALEGKG
IMLRSEWDVL PFLESGKLVQ VLPEYAQSAN IWAVYREPLY RSMKLRVCVE FLAAWCQQRL
GKPDEGYQVM
Length

310

Mol. Wt

35.314 kDa

pI

6.5 (calculated)

Extinction coefficient

49,390 - 50,140 (calc based on 11 Y, 6 W, and 6 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

91..297

PF03466 LysR substrate binding domain

PMID:19920124[9]

Domain

8..67

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

PMID:19920124[9]

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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=ttdR taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130956

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947562

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010045

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P45463

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12694

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12694

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947562

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002359

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2557

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
  6. ↑ 6.0 6.1 6.2 Oshima, T & Biville, F (2006) Functional identification of ygiP as a positive regulator of the ttdA-ttdB-ygjE operon. Microbiology (Reading, Engl.) 152 2129-35 PubMed
  7. ↑ 7.0 7.1 7.2 Kim, OB et al. (2009) Regulation of tartrate metabolism by TtdR and relation to the DcuS-DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli. Microbiology (Reading, Engl.) 155 3632-40 PubMed
  8. ↑ 8.0 8.1 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.0 9.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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