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Protein

HTH-type transcriptional regulator RutR

Gene

rutR

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Master transcription regulator which represses the degradation of pyrimidines (rutABCDEFG) and purines (gcl operon) for maintenance of metabolic balance between pyrimidines and purines. It also regulates the synthesis of pyrimidine nucleotides and arginine from glutamine (carAB) and the supply of glutamate (gadABWX).2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi39 – 5820H-T-H motifPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of transcription, DNA-templated Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:PD01352.
ECOL316407:JW0998-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
HTH-type transcriptional regulator RutR
Alternative name(s):
Rut operon repressor
Gene namesi
Name:rutR
Synonyms:ycdC
Ordered Locus Names:b1013, JW0998
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12301. rutR.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 212212HTH-type transcriptional regulator RutRPRO_0000070635Add
BLAST

Proteomic databases

PaxDbiP0ACU2.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000870.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
kdsBP049512EBI-1121539,EBI-544810

Protein-protein interaction databases

IntActiP0ACU2. 23 interactions.
STRINGi511145.b1013.

Structurei

Secondary structure

1
212
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi14 – 3421Combined sources
Turni36 – 383Combined sources
Helixi41 – 488Combined sources
Helixi52 – 587Combined sources
Beta strandi59 – 613Combined sources
Helixi62 – 8221Combined sources
Helixi90 – 10718Combined sources
Helixi109 – 12012Combined sources
Turni124 – 1263Combined sources
Helixi127 – 1315Combined sources
Helixi133 – 15018Combined sources
Helixi159 – 17517Combined sources
Helixi177 – 1848Combined sources
Helixi191 – 20919Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LOCX-ray2.50A/B/C/D1-212[»]
4JYKX-ray1.70A/B1-212[»]
4X1EX-ray2.40A/B1-212[»]
4XK4X-ray2.27A/B/C/D1-212[»]
ProteinModelPortaliP0ACU2.
SMRiP0ACU2. Positions 12-212.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini17 – 7761HTH tetR-typePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 HTH tetR-type DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108R86. Bacteria.
COG1309. LUCA.
HOGENOMiHOG000267645.
InParanoidiP0ACU2.
KOiK09017.
OMAiFCLEMIQ.
OrthoDBiEOG6HF5ZN.
PhylomeDBiP0ACU2.

Family and domain databases

Gene3Di1.10.10.60. 2 hits.
1.10.357.10. 1 hit.
InterProiIPR009057. Homeodomain-like.
IPR001647. HTH_TetR.
IPR015893. Tet_transcr_reg_TetR-like_C.
IPR011075. Tet_transcr_reg_TetR-rel_C.
IPR019915. Tscrpt_reg_pyr_util_RutR.
IPR013573. Tscrpt_reg_YcdC_C.
[Graphical view]
PfamiPF08362. TetR_C_3. 1 hit.
PF00440. TetR_N. 1 hit.
[Graphical view]
PRINTSiPR00455. HTHTETR.
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF48498. SSF48498. 1 hit.
TIGRFAMsiTIGR03613. RutR. 1 hit.
PROSITEiPS50977. HTH_TETR_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ACU2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQGAVKTTG KRSRAVSAKK KAILSAALDT FSQFGFHGTR LEQIAELAGV
60 70 80 90 100
SKTNLLYYFP SKEALYIAVL RQILDIWLAP LKAFREDFAP LAAIKEYIRL
110 120 130 140 150
KLEVSRDYPQ ASRLFCMEML AGAPLLMDEL TGDLKALIDE KSALIAGWVK
160 170 180 190 200
SGKLAPIDPQ HLIFMIWAST QHYADFAPQV EAVTGATLRD EVFFNQTVEN
210
VQRIIIEGIR PR
Length:212
Mass (Da):23,688
Last modified:November 22, 2005 - v1
Checksum:iE2459B85DFAC277A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74098.1.
AP009048 Genomic DNA. Translation: BAA35790.1.
PIRiC64843.
RefSeqiNP_415533.1. NC_000913.3.
WP_000191701.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74098; AAC74098; b1013.
BAA35790; BAA35790; BAA35790.
GeneIDi945075.
KEGGiecj:JW0998.
eco:b1013.
PATRICi32117255. VBIEscCol129921_1051.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74098.1.
AP009048 Genomic DNA. Translation: BAA35790.1.
PIRiC64843.
RefSeqiNP_415533.1. NC_000913.3.
WP_000191701.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3LOCX-ray2.50A/B/C/D1-212[»]
4JYKX-ray1.70A/B1-212[»]
4X1EX-ray2.40A/B1-212[»]
4XK4X-ray2.27A/B/C/D1-212[»]
ProteinModelPortaliP0ACU2.
SMRiP0ACU2. Positions 12-212.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0ACU2. 23 interactions.
STRINGi511145.b1013.

Proteomic databases

PaxDbiP0ACU2.

Protocols and materials databases

DNASUi945075.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74098; AAC74098; b1013.
BAA35790; BAA35790; BAA35790.
GeneIDi945075.
KEGGiecj:JW0998.
eco:b1013.
PATRICi32117255. VBIEscCol129921_1051.

Organism-specific databases

EchoBASEiEB2207.
EcoGeneiEG12301. rutR.

Phylogenomic databases

eggNOGiENOG4108R86. Bacteria.
COG1309. LUCA.
HOGENOMiHOG000267645.
InParanoidiP0ACU2.
KOiK09017.
OMAiFCLEMIQ.
OrthoDBiEOG6HF5ZN.
PhylomeDBiP0ACU2.

Enzyme and pathway databases

BioCyciEcoCyc:PD01352.
ECOL316407:JW0998-MONOMER.

Miscellaneous databases

PROiP0ACU2.

Gene expression databases

CollecTFiEXPREG_00000870.

Family and domain databases

Gene3Di1.10.10.60. 2 hits.
1.10.357.10. 1 hit.
InterProiIPR009057. Homeodomain-like.
IPR001647. HTH_TetR.
IPR015893. Tet_transcr_reg_TetR-like_C.
IPR011075. Tet_transcr_reg_TetR-rel_C.
IPR019915. Tscrpt_reg_pyr_util_RutR.
IPR013573. Tscrpt_reg_YcdC_C.
[Graphical view]
PfamiPF08362. TetR_C_3. 1 hit.
PF00440. TetR_N. 1 hit.
[Graphical view]
PRINTSiPR00455. HTHTETR.
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF48498. SSF48498. 1 hit.
TIGRFAMsiTIGR03613. RutR. 1 hit.
PROSITEiPS50977. HTH_TETR_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: FUNCTION IN PYRIMIDINE CATABOLISM, NOMENCLATURE.
    Strain: K12 / MG1655 / ATCC 47076.
  5. "RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines."
    Shimada T., Hirao K., Kori A., Yamamoto K., Ishihama A.
    Mol. Microbiol. 66:744-757(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TRANSCRIPTIONAL REGULATOR.
  6. "Crystal structure of hypothetical transcriptional regulator ycdC from Escherichia coli."
    New York structural genomics research consortium (NYSGRC)
    Submitted (MAY-2003) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiRUTR_ECOLI
AccessioniPrimary (citable) accession number: P0ACU2
Secondary accession number(s): P75899
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 22, 2005
Last modified: July 6, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The Rut pathway degrades exogenous pyrimidines as the sole nitrogen source at room temperature but not at 37 degrees Celsius, a restriction that is apparently a consequence of an inadequate ability to remove toxic malonic semialdehyde at the higher temperature (RutE/YdfG function).

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.