Escherichia coli K-12 substr. MG1655 Polypeptide: RtcR DNA-binding transcriptional activator

Gene: rtcR Accession Numbers: EG12356 (EcoCyc), b3422, ECK3408

Synonyms: yhgB

Regulation Summary Diagram: ?

Regulation summary diagram for rtcR

RtcR , "RNA terminal phosphate cyclase regulator," regulates the expression of genes involved in the ATP-dependent conversion of a 3'-phosphate at the end of RNA to 2',3'-cyclic phosphodiester [Genschik98].

RtcR belongs to the group of σ54-dependent transcriptional regulators, which contain three domains: the sensory domain located in the N terminus, the central domain involved in ATP hydrolysis and interaction with σ54, and the C-terminal domain, which contains a helix-turn-helix motif. Although the C-terminal domain and the central domain from RtcR are similar to those of other members of this group, its N-terminal domain is not [Genschik98].

The rtcR gene is transcribed divergently from the genes it regulates [Genschik98].

Locations: cytosol

Map Position: [3,556,290 -> 3,557,888] (76.65 centisomes, 276°)
Length: 1599 bp / 532 aa

Molecular Weight of Polypeptide: 60.299 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011174 , DIP:DIP-10812N , EchoBASE:EB2259 , EcoGene:EG12356 , EcoliWiki:b3422 , ModBase:P38035 , OU-Microarray:b3422 , PortEco:rtcR , PR:PRO_000023893 , Pride:P38035 , Protein Model Portal:P38035 , RefSeq:NP_417880 , RegulonDB:EG12356 , SMR:P38035 , String:511145.b3422 , UniProt:P38035

Relationship Links: InterPro:IN-FAMILY:IPR002078 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR009715 , InterPro:IN-FAMILY:IPR017183 , InterPro:IN-FAMILY:IPR025943 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR32071:SF14 , Pfam:IN-FAMILY:PF00158 , Pfam:IN-FAMILY:PF06956 , Prosite:IN-FAMILY:PS00676 , Prosite:IN-FAMILY:PS50045 , Smart:IN-FAMILY:SM00382

In Paralogous Gene Group: 105 (10 members)

GO Terms:

Biological Process: GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [Genschik98]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11, Gaudet10]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0000156 - phosphorelay response regulator activity Inferred by computational analysis [Gaudet10]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01, Gaudet10, Genschik98]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0008134 - transcription factor binding Inferred by computational analysis [GOA01]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [Gaudet10]
GO:0044212 - transcription regulatory region DNA binding Inferred by computational analysis [Gaudet10]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [UniProtGOA11, Gaudet10]
GO:0005737 - cytoplasm Inferred by curator
GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related Transcription related
regulation genetic unit regulated operon
regulation type of regulation transcriptional level

Symmetry: Inverted Repeat

Regulated Transcription Units (1 total): ?


Transcription-unit diagram

Essentiality data for rtcR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Curated 22-Dec-2005 by Keseler I , SRI International
Last-Curated ? 28-May-2008 by Gama-Castro S , UNAM

Sequence Features

Protein sequence of RtcR DNA-binding transcriptional activator with features indicated

Feature Class Location Citations Comment
Conserved-Region 186 -> 424
UniProt: Sigma-54 factor interaction;
Nucleotide-Phosphate-Binding-Region 215 -> 222
UniProt: ATP; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 281 -> 290
UniProt: ATP; Non-Experimental Qualifier: potential;
DNA-Binding-Region 485 -> 504
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3422 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12356; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Genschik98: Genschik P, Drabikowski K, Filipowicz W (1998). "Characterization of the Escherichia coli RNA 3'-terminal phosphate cyclase and its sigma54-regulated operon." J Biol Chem 273(39);25516-26. PMID: 9738023

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Mon Oct 5, 2015, biocyc13.