rutR: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

YcdC

Synonyms

predicted DNA-binding transcriptional regulator[1], B1013[2][1], YcdC[2][1], RutR[2][1] , ECK1004, JW0998, ycdC, b1013

Product description

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

Repressor for divergent rut operon; pyrimidine nitrogen catabolism[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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001647

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:15944459[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:17919280[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:18515344[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:15944459[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:17919280[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:18515344[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR015893

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:15944459[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:17919280[6]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:18515344[7]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:15944459[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:17919280[6]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:18515344[7]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:15944459[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:17919280[6]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:18515344[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

rpsI

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

uspG

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

purR

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rpsM

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

glpC

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rpsG

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rpmE

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

ynaE

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rpmB

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

slyD

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

pqqL

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rplQ

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rplB

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

ompL

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

insO2

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rplA

PMID:16606699[8]

Experiment(s):EBI-1138623

Protein

rpsT

PMID:16606699[8]

Experiment(s):EBI-1138623
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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 

MTQGAVKTTG KRSRAVSAKK KAILSAALDT FSQFGFHGTR LEQIAELAGV SKTNLLYYFP
SKEALYIAVL RQILDIWLAP LKAFREDFAP LAAIKEYIRL KLEVSRDYPQ ASRLFCMEML
AGAPLLMDEL TGDLKALIDE KSALIAGWVK SGKLAPIDPQ HLIFMIWAST QHYADFAPQV
EAVTGATLRD EVFFNQTVEN VQRIIIEGIR PR
Length

212

Mol. Wt

23.688 kDa

pI

9.2 (calculated)

Extinction coefficient

25,440 - 25,565 (calc based on 6 Y, 3 W, and 1 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

23..69

PF00440 Bacterial regulatory proteins, tetR family

PMID:19920124[9]

Domain

70..212

PF08362 YcdC-like protein, C-terminal region

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=rutR 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:16128979

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945075

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003422

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACU2

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12301

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12301

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945075

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002180

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2207

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 5.2 5.3 5.4 Ramos, JL et al. (2005) The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69 326-56 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Shimada, T et al. (2007) RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Mol. Microbiol. 66 744-57 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Shimada, T et al. (2008) The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res. 36 3950-5 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 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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