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Protein

Transcriptional regulatory protein TyrR

Gene

tyrR

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

Functioni

Involved in transcriptional regulation of aromatic amino acid biosynthesis and transport. Modulates the expression of at least 8 unlinked operons. Seven of these operons are regulated in response to changes in the concentration of the three aromatic amino acids (phenylalanine, tyrosine and tryptophan). These amino acids are suggested to act as co-effectors which bind to the TyrR protein to form an active regulatory protein. In most cases TyrR causes negative regulation, but positive effects on the tyrP gene have been observed at high phenylalanine concentrations.

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi234 – 2418ATPPROSITE-ProRule annotation
Nucleotide bindingi290 – 29910ATPPROSITE-ProRule annotation
DNA bindingi483 – 50220H-T-H motifSequence analysisAdd
BLAST

GO - Molecular functioni

  • amino acid binding Source: InterPro
  • ATP binding Source: EcoCyc
  • DNA binding Source: EcoCyc

GO - Biological processi

  • aromatic compound catabolic process Source: UniProtKB-KW
  • negative regulation of transcription, DNA-templated Source: EcoCyc
  • phosphorelay signal transduction system Source: UniProtKB-KW
  • regulation of transcription, DNA-templated Source: EcoCyc
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Aromatic hydrocarbons catabolism, Transcription, Transcription regulation, Two-component regulatory system

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:PD00413.
ECOL316407:JW1316-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcriptional regulatory protein TyrR
Gene namesi
Name:tyrR
Ordered Locus Names:b1323, JW1316
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11042. tyrR.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 513513Transcriptional regulatory protein TyrRPRO_0000081339Add
BLAST

Proteomic databases

EPDiP07604.
PaxDbiP07604.

Interactioni

Subunit structurei

Homodimer. In presence of tyrosine (to the lesser extent, phenylalanine or tryptophan) and excess of ATP it undergoes a ligand-induced hexamerization. It is suggested that the hexameric form of TyrR is the active repressing species, interacting with two or three tyrR boxes in the targeted regulatory DNA.2 Publications

Protein-protein interaction databases

BioGridi4260150. 9 interactions.
DIPiDIP-11062N.
IntActiP07604. 4 interactions.
MINTiMINT-1240380.
STRINGi511145.b1323.

Structurei

Secondary structure

1
513
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 76Combined sources
Helixi13 – 2311Combined sources
Beta strandi28 – 347Combined sources
Turni35 – 373Combined sources
Beta strandi38 – 436Combined sources
Helixi48 – 6013Combined sources
Beta strandi64 – 718Combined sources
Turni74 – 763Combined sources
Helixi77 – 8812Combined sources
Beta strandi93 – 964Combined sources
Beta strandi101 – 1055Combined sources
Helixi107 – 1137Combined sources
Helixi117 – 1204Combined sources
Helixi125 – 1273Combined sources
Helixi134 – 1396Combined sources
Beta strandi146 – 1527Combined sources
Beta strandi155 – 16410Combined sources
Turni165 – 1684Combined sources
Beta strandi169 – 1768Combined sources
Helixi178 – 1858Combined sources
Turni186 – 1883Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JHEX-ray2.30A/B/C/D1-190[»]
ProteinModelPortaliP07604.
SMRiP07604. Positions 1-508.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP07604.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 7271ACTPROSITE-ProRule annotationAdd
BLAST
Domaini78 – 14972PASPROSITE-ProRule annotationAdd
BLAST
Domaini206 – 428223Sigma-54 factor interactionPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 ACT domain.PROSITE-ProRule annotation
Contains 1 PAS (PER-ARNT-SIM) domain.PROSITE-ProRule annotation
Contains 1 sigma-54 factor interaction domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4108JU8. Bacteria.
COG3283. LUCA.
HOGENOMiHOG000058487.
InParanoidiP07604.
KOiK03721.
OMAiIANPASC.
OrthoDBiEOG6WHNMG.
PhylomeDBiP07604.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR002912. ACT_dom.
IPR009057. Homeodomain-like.
IPR030828. HTH_TypR.
IPR027417. P-loop_NTPase.
IPR000014. PAS.
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]
PfamiPF13188. PAS_8. 1 hit.
PF00158. Sigma54_activat. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00091. PAS. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR04381. HTH_TypR. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
PS50112. PAS. 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.

P07604-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRLEVFCEDR LGLTRELLDL LVLRGIDLRG IEIDPIGRIY LNFAELEFES
60 70 80 90 100
FSSLMAEIRR IAGVTDVRTV PWMPSEREHL ALSALLEALP EPVLSVDMKS
110 120 130 140 150
KVDMANPASC QLFGQKLDRL RNHTAAQLIN GFNFLRWLES EPQDSHNEHV
160 170 180 190 200
VINGQNFLME ITPVYLQDEN DQHVLTGAVV MLRSTIRMGR QLQNVAAQDV
210 220 230 240 250
SAFSQIVAVS PKMKHVVEQA QKLAMLSAPL LITGDTGTGK DLFAYACHQA
260 270 280 290 300
SPRAGKPYLA LNCASIPEDA VESELFGHAP EGKKGFFEQA NGGSVLLDEI
310 320 330 340 350
GEMSPRMQAK LLRFLNDGTF RRVGEDHEVH VDVRVICATQ KNLVELVQKG
360 370 380 390 400
MFREDLYYRL NVLTLNLPPL RDCPQDIMPL TELFVARFAD EQGVPRPKLA
410 420 430 440 450
ADLNTVLTRY AWPGNVRQLK NAIYRALTQL DGYELRPQDI LLPDYDAATV
460 470 480 490 500
AVGEDAMEGS LDEITSRFER SVLTQLYRNY PSTRKLAKRL GVSHTAIANK
510
LREYGLSQKK NEE
Length:513
Mass (Da):57,656
Last modified:November 1, 1991 - v2
Checksum:iB580A401C3A27866
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12114 Genomic DNA. Translation: AAA24706.1.
U00096 Genomic DNA. Translation: AAC74405.1.
AP009048 Genomic DNA. Translation: BAA14905.1.
PIRiA47086. RGECAY.
RefSeqiNP_415839.1. NC_000913.3.
WP_001300658.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74405; AAC74405; b1323.
BAA14905; BAA14905; BAA14905.
GeneIDi945879.
KEGGiecj:JW1316.
eco:b1323.
PATRICi32117920. VBIEscCol129921_1380.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M12114 Genomic DNA. Translation: AAA24706.1.
U00096 Genomic DNA. Translation: AAC74405.1.
AP009048 Genomic DNA. Translation: BAA14905.1.
PIRiA47086. RGECAY.
RefSeqiNP_415839.1. NC_000913.3.
WP_001300658.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JHEX-ray2.30A/B/C/D1-190[»]
ProteinModelPortaliP07604.
SMRiP07604. Positions 1-508.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260150. 9 interactions.
DIPiDIP-11062N.
IntActiP07604. 4 interactions.
MINTiMINT-1240380.
STRINGi511145.b1323.

Proteomic databases

EPDiP07604.
PaxDbiP07604.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74405; AAC74405; b1323.
BAA14905; BAA14905; BAA14905.
GeneIDi945879.
KEGGiecj:JW1316.
eco:b1323.
PATRICi32117920. VBIEscCol129921_1380.

Organism-specific databases

EchoBASEiEB1035.
EcoGeneiEG11042. tyrR.

Phylogenomic databases

eggNOGiENOG4108JU8. Bacteria.
COG3283. LUCA.
HOGENOMiHOG000058487.
InParanoidiP07604.
KOiK03721.
OMAiIANPASC.
OrthoDBiEOG6WHNMG.
PhylomeDBiP07604.

Enzyme and pathway databases

BioCyciEcoCyc:PD00413.
ECOL316407:JW1316-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP07604.
PROiP07604.

Family and domain databases

Gene3Di1.10.10.60. 1 hit.
3.40.50.300. 1 hit.
InterProiIPR003593. AAA+_ATPase.
IPR002912. ACT_dom.
IPR009057. Homeodomain-like.
IPR030828. HTH_TypR.
IPR027417. P-loop_NTPase.
IPR000014. PAS.
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]
PfamiPF13188. PAS_8. 1 hit.
PF00158. Sigma54_activat. 1 hit.
[Graphical view]
SMARTiSM00382. AAA. 1 hit.
SM00091. PAS. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF52540. SSF52540. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR04381. HTH_TypR. 1 hit.
PROSITEiPS51671. ACT. 1 hit.
PS50112. PAS. 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...

Publicationsi

« Hide 'large scale' publications
  1. "Structure of the Escherichia coli K12 regulatory gene tyrR. Nucleotide sequence and sites of initiation of transcription and translation."
    Cornish E.C., Argyropoulos V.P., Pittard J., Davidson B.E.
    J. Biol. Chem. 261:403-410(1986) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Ganesan S.
    Thesis (1989), University of Melbourne, Australia
    Cited for: SEQUENCE REVISION.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  5. "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.
  6. "A genetic analysis of various functions of the TyrR protein of Escherichia coli."
    Yang J., Ganesan S., Sarsero J., Pittard A.J.
    J. Bacteriol. 175:1767-1776(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "The TyrR protein of Escherichia coli, analysis by limited proteolysis of domain structure and ligand-mediated conformational changes."
    Cui J., Somerville R.L.
    J. Biol. Chem. 268:5040-5047(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: DOMAINS, PARTIAL PROTEIN SEQUENCE.
  8. "Purification of the Escherichia coli regulatory protein TyrR and analysis of its interactions with ATP, tyrosine, phenylalanine, and tryptophan."
    Argaet V.P., Wilson T.J., Davidson B.E.
    J. Biol. Chem. 269:5171-5178(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  9. "Ligand-induced self-association of the Escherichia coli regulatory protein TyrR."
    Wilson T.J., Maroudas P., Howlett G.J., Davidson B.E.
    J. Mol. Biol. 238:309-318(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  10. "The effect of self-association on the interaction of the Escherichia coli regulatory protein TyrR with DNA."
    Bailey M.F., Davidson B.E., Minton A.P., Sawyer W.H., Howlett G.J.
    J. Mol. Biol. 263:671-684(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  11. "TyrR protein of Escherichia coli and its role as repressor and activator."
    Pittard A.J., Davidson B.E.
    Mol. Microbiol. 5:1585-1592(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiTYRR_ECOLI
AccessioniPrimary (citable) accession number: P07604
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1988
Last sequence update: November 1, 1991
Last modified: March 16, 2016
This is version 148 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The tyrR gene is autogenously regulated by a mechanism that gives similar rates of expression of tyrR irrespective of concentration of the aromatic amino acids.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.