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



Gene: cbl Accession Numbers: G7071 (EcoCyc), b1987, ECK1982

Regulation Summary Diagram: ?

Component of: Cbl-APS (summary available)

Summary:
The transcription factor Cbl, for "cysB like," is a regulator involved in the expression of genes required for aliphatic sulfonate utilization and homeostatic response to sulfate starvation [vanderPloeg97, vanDer99, IwanickaNowicka95, Kertesz00, vanderPloeg01, Bykowski02]. Cbl does not require a ligand to binds to its DNA-binding site, but the activity of this protein is negatively regulated by the 5'-phophosulfate cofactor [Bykowski02].

This protein belongs to the large LysR family of transcriptional regulators and it is positively regulated by CysB, which is similar to Cbl (40% identity) [IwanickaNowicka95, Stec04]. Members of this family have two domains, an N-terminal domain with a helix-turn-helix DNA-binding motif and a large C-terminal domain [IwanickaNowicka95, Stec04, Stec06]. In systematic studies of oligomerization, it was shown that some members of the LysR family, like Cbl, interact with other members of the family to form heterodimers, but the physiological significance of this is unknown [Knapp10].

The crystal structure of the C-terminal regulatory domain of Cbl (2.8Å) has been solved [Stec06].

Locations: cytosol

Map Position: [2,057,988 <- 2,058,938] (44.36 centisomes)
Length: 951 bp / 316 aa

Molecular Weight of Polypeptide: 35.856 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006590 , DIP:DIP-9248N , EchoBASE:EB4012 , EcoGene:EG14264 , EcoliWiki:b1987 , ModBase:Q47083 , OU-Microarray:b1987 , PortEco:cbl , PR:PRO_000022249 , Pride:Q47083 , Protein Model Portal:Q47083 , RefSeq:NP_416492 , RegulonDB:G7071 , SMR:Q47083 , String:511145.b1987 , Swiss-Model:Q47083 , UniProt:Q47083

Relationship Links: InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011991 , PDB:Structure:2FYI , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Paralogous Gene Group: 6 (42 members)

In Reactions of unknown directionality:

Not in pathways:
Cbl + adenosine 5'-phosphosulfate = Cbl-APS

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0045883 - positive regulation of sulfur utilization Inferred from experiment [vanDer99]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids cysteine
metabolism metabolism of other compounds sulfur metabolism
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator

DNA binding site length: 40 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (2 total): ?

Notes:

Essentiality data for cbl knockouts: ?

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

Subunit of: Cbl-APS

Synonyms: MetC, B1987, Cbl

Subunit composition of Cbl-APS = [Cbl][adenosine 5'-phosphosulfate]
         Cbl DNA-binding transcriptional activator = Cbl (extended summary available)

Summary:
The activity of Cbl transcriptional regulator is inhibited by adenosine-5' -phosphosulphate (APS) . It was suggested that this inhibition is a result of a change in Cbl conformation that is unfavorable for the recruitment of the RNA polymerase[Bykowski02].

Sequence Length: 316 AAs

In Reactions of unknown directionality:

Not in pathways:
Cbl + adenosine 5'-phosphosulfate = Cbl-APS

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids cysteine
metabolism metabolism of other compounds sulfur metabolism
regulation genetic unit regulated regulon
regulation type of regulation transcriptional level activator


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 59
[UniProt09]
UniProt: HTH lysR-type;
DNA-Binding-Region 19 -> 38
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 143
[IwanickaNowicka95, UniProt10a]
Alternate sequence: A → R; UniProt: (in Ref. 1; AAA99929);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Bykowski02: Bykowski T, van der Ploeg JR, Iwanicka-Nowicka R, Hryniewicz MM (2002). "The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5'-phosphosulphate (APS) as a signalling molecule for sulphate excess." Mol Microbiol 43(5);1347-58. PMID: 11918818

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

IwanickaNowicka95: Iwanicka-Nowicka R, Hryniewicz MM (1995). "A new gene, cbl, encoding a member of the LysR family of transcriptional regulators belongs to Escherichia coli cys regulon." Gene 1995;166(1);11-7. PMID: 8529872

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

Kertesz00: Kertesz MA (2000). "Riding the sulfur cycle--metabolism of sulfonates and sulfate esters in gram-negative bacteria." FEMS Microbiol Rev 24(2);135-75. PMID: 10717312

Knapp10: Knapp GS, Hu JC (2010). "Specificity of the E. coli LysR-type transcriptional regulators." PLoS One 5(12);e15189. PMID: 21187915

Stec04: Stec E, Witkowska M, Hryniewicz MM, Brzozowski AM, Wilkinson AJ, Bujacz GD (2004). "Crystallization and preliminary crystallographic studies of the cofactor-binding domain of the LysR-type transcriptional regulator Cbl from Escherichia coli." Acta Crystallogr D Biol Crystallogr 60(Pt 9);1654-7. PMID: 15333946

Stec06: Stec E, Witkowska-Zimny M, Hryniewicz MM, Neumann P, Wilkinson AJ, Brzozowski AM, Verma CS, Zaim J, Wysocki S, Bujacz GD (2006). "Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactor-binding domain of the Cbl transcriptional regulator." J Mol Biol 364(3);309-22. PMID: 17010379

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.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

vanDer99: van Der Ploeg JR, Iwanicka-Nowicka R, Bykowski T, Hryniewicz MM, Leisinger T (1999). "The Escherichia coli ssuEADCB gene cluster is required for the utilization of sulfur from aliphatic sulfonates and is regulated by the transcriptional activator Cbl." J Biol Chem 274(41);29358-65. PMID: 10506196

vanderPloeg01: van der Ploeg JR, Eichhorn E, Leisinger T (2001). "Sulfonate-sulfur metabolism and its regulation in Escherichia coli." Arch Microbiol 176(1-2);1-8. PMID: 11479697

vanderPloeg97: van der Ploeg JR, Iwanicka-Nowicka R, Kertesz MA, Leisinger T, Hryniewicz MM (1997). "Involvement of CysB and Cbl regulatory proteins in expression of the tauABCD operon and other sulfate starvation-inducible genes in Escherichia coli." J Bacteriol 179(24);7671-8. PMID: 9401024

Other References Related to Gene Regulation

Zimmer00: Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S (2000). "Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation." Proc Natl Acad Sci U S A 97(26);14674-9. PMID: 11121068


Report Errors or Provide Feedback
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 18.5 on Thu Nov 27, 2014, BIOCYC14A.