Escherichia coli K-12 substr. MG1655 Protein: AllR-allantoin

Gene: allR Accession Numbers: G6276 (EcoCyc), b0506, ECK0499

Synonyms: glxA3, ybbU

Regulation Summary Diagram: ?

Regulation summary diagram for allR

Subunit composition of AllR-allantoin = [allantoin][AllR]
         AllR DNA-binding transcriptional repressor = AllR (extended summary available)

Gene Citations: [Cusa99]

Map Position: [532,235 -> 533,050] (11.47 centisomes, 41°)
Length: 816 bp / 271 aa

Unification Links: ASAP:ABE-0001750 , EchoBASE:EB3382 , EcoGene:EG13616 , OU-Microarray:b0506 , PortEco:allR , RegulonDB:G6276

In Reactions of unknown directionality:

Not in pathways:
allantoin + AllR = AllR-allantoin

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

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

DNA binding site length: 17 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TTGGAAaAaTaTTCCAA

Regulated Transcription Units (3 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Subunit of AllR-allantoin: AllR DNA-binding transcriptional repressor

Synonyms: YbbU, AllR

Gene: allR Accession Numbers: G6276 (EcoCyc), b0506, ECK0499

Locations: cytosol

Sequence Length: 271 AAs

Molecular Weight: 29.27 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred by computational analysis Inferred from experiment [Cusa99, Walker06]
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:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis Inferred from experiment [Cusa99, Walker06]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0042802 - identical protein binding Inferred from experiment [Rajagopala14]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, Gaudet10, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by curator
GO:0032993 - protein-DNA complex Inferred by computational analysis [Gaudet10]

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

Unification Links: DIP:DIP-47907N , EcoliWiki:b0506 , ModBase:P0ACN4 , PR:PRO_000022083 , Pride:P0ACN4 , Protein Model Portal:P0ACN4 , RefSeq:NP_415039 , SMR:P0ACN4 , String:511145.b0506 , UniProt:P0ACN4

Relationship Links: InterPro:IN-FAMILY:IPR005471 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014757 , InterPro:IN-FAMILY:IPR029016 , PDB:Structure:1TF1 , Pfam:IN-FAMILY:PF01614 , Pfam:IN-FAMILY:PF09339 , Prosite:IN-FAMILY:PS51077 , Prosite:IN-FAMILY:PS51078 , Smart:IN-FAMILY:SM00346

In Reactions of unknown directionality:

Not in pathways:
allantoin + AllR = AllR-allantoin
AllR + glyoxylate = AllR-glyox

AllR (for "allantoin repressor") regulates several genes involved in the anaerobic utilization of allantoin as a nitrogen source [Cusa99, Rintoul02].

At very low concentrations of glyoxylate, AllR represses transcription from allAp, allSp, and gclp. A highly conserved region featuring an almost perfect palindromic sequence has been identified in gclp and in the intergenic region between the divergent promoters allAp and allSp. It has been proven that AllR binds to this region, and it has been proposed that it may interfere with RNA polymerase by steric hindrance or contact inhibition, thus repressing transcription. In the presence of glyoxylate (the coeffector molecule of this regulator), DNA binding by AllR is inhibited and transcription of the allantoin regulon is derepressed [Rintoul02, Walker06].

AllR belongs to the IclR family. Members of this family of regulators feature a conserved domain architecture, with a DNA-binding motif in the N-terminal domain and a ligand-binding motif in the C-terminal domain. This regulator adopts a tetrameric conformation [Rintoul02, Walker06].

The allR gene is expressed under both aerobic and anaerobic conditions, and it is autoregulated [Walker06].

Essentiality data for allR 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]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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


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

Cusa99: Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J (1999). "Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli." J Bacteriol 1999;181(24);7479-84. PMID: 10601204

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

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

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

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

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Rintoul02: Rintoul MR, Cusa E, Baldoma L, Badia J, Reitzer L, Aguilar J (2002). "Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS." J Mol Biol 324(4);599-610. PMID: 12460564

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

Walker06: Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A (2006). "Structural and biochemical study of effector molecule recognition by the E.coli glyoxylate and allantoin utilization regulatory protein AllR." J Mol Biol 358(3);810-28. PMID: 16546208

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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 Sun Oct 4, 2015, BIOCYC14A.