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Escherichia coli K-12 substr. MG1655 Protein: PurR transcriptional repressor



Gene: purR Accession Numbers: EG10800 (EcoCyc), b1658, ECK1654

Regulation Summary Diagram: ?

Component of: PurR-Hypoxanthine DNA-binding transcriptional repressor

Subunit composition of PurR transcriptional repressor = [PurR]2

Summary:
PurR dimer controls several genes involved in purine nucleotide biosynthesis and its own synthesis [Choi92][He90, Rolfes90, Meng90]. This regulator necessarily binds two products of purine metabolism, hypoxanthine and guanine, to induce the conformational change that allows PurR to bind DNA [Choi92, Meng90a, Rolfes90a].

PurR belongs to the GalR/LacI family [FukamiKobayashi03], and it shows 35%, 33%, and 26% identity with CytR, GalR, and LacI, respectively [Rolfes88]. As with other members of this group, PurR shows a helix-turn-helix motif in the N-terminal domain for DNA binding [Rolfes88, Choi92] and a ligand-binding and dimerization motif in the C-terminal domain that shows similarity with ligand binding sites of periplasmic sugar-binding proteins [Choi92][Schumacher93, FukamiKobayashi03]. The two domains are connected by a hinge sequence that is also important for DNA binding and that can be cleavage by proteases when the protein is not bound to DNA [Choi94, SwintKruse02].

The members of the GalR/LacI family also have a partial conservation in their DNA-binding motif which has an imperfect dyad symmetry [Rolfes88]. The nonconserved nucleotides in the motif give specificity to each regulator [Rolfes88].

Except for the purR gene and purA, which both have two DNA-binding sites for PurR, all genes regulated by PurR in Escherichia coli have only one DNA-binding motif to bind the regulator [Rolfes90].

Based on ChIP-chip, gene expression, and computational analyses, new members of the PurR regulon have been identified [Cho11].

Locations: cytosol

Map Position: [1,735,868 -> 1,736,893] (37.41 centisomes)
Length: 1026 bp / 341 aa

Molecular Weight of Polypeptide: 38.175 kD (from nucleotide sequence)

pI: 6.55

Unification Links: ASAP:ABE-0005545 , CGSC:17989 , DIP:DIP-35931N , EchoBASE:EB0793 , EcoGene:EG10800 , EcoliWiki:b1658 , OU-Microarray:b1658 , PortEco:purR , PR:PRO_000023644 , Pride:P0ACP7 , Protein Model Portal:P0ACP7 , RefSeq:NP_416175 , RegulonDB:EG10800 , SMR:P0ACP7 , String:511145.b1658 , UniProt:P0ACP7

Relationship Links: InterPro:IN-FAMILY:IPR000843 , InterPro:IN-FAMILY:IPR010982 , InterPro:IN-FAMILY:IPR023588 , InterPro:IN-FAMILY:IPR026909 , InterPro:IN-FAMILY:IPR028082 , Panther:IN-FAMILY:PTHR30146:SF7 , PDB:Structure:1BDH , PDB:Structure:1BDI , PDB:Structure:1DBQ , PDB:Structure:1JFS , PDB:Structure:1JFT , PDB:Structure:1JH9 , PDB:Structure:1JHZ , PDB:Structure:1PNR , PDB:Structure:1PRU , PDB:Structure:1PRV , PDB:Structure:1QP0 , PDB:Structure:1QP4 , PDB:Structure:1QP7 , PDB:Structure:1QPZ , PDB:Structure:1QQA , PDB:Structure:1QQB , PDB:Structure:1VPW , PDB:Structure:1WET , PDB:Structure:1ZAY , PDB:Structure:2PUA , PDB:Structure:2PUB , PDB:Structure:2PUC , PDB:Structure:2PUD , PDB:Structure:2PUE , PDB:Structure:2PUF , PDB:Structure:2PUG , Pfam:IN-FAMILY:PF00356 , Prints:IN-FAMILY:PR00036 , Prosite:IN-FAMILY:PS00356 , Prosite:IN-FAMILY:PS50932 , Smart:IN-FAMILY:SM00354

In Paralogous Gene Group: 30 (25 members)

In Reactions of unknown directionality:

Not in pathways:
PurR + hypoxanthine = PurR-hypoxanthine

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006164 - purine nucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Choi92]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0045892 - negative regulation of transcription, DNA-templated Inferred by computational analysis [GOA06]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, He90]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: extrachromosomal colicin related
information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids histidine
metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone
metabolism biosynthesis of building blocks nucleotides purine biosynthesis
metabolism biosynthesis of building blocks nucleotides pyrimidine biosynthesis
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
metabolism central intermediary metabolism nucleotide and nucleoside conversions
metabolism central intermediary metabolism polyamine biosynthesis
metabolism metabolism of other compounds nitrogen metabolism
regulation genetic unit regulated regulon
regulation
regulation type of regulation transcriptional level repressor

Essentiality data for purR 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]

Credits:
Revised 23-May-2011 by Brito D


Subunit of: PurR-Hypoxanthine DNA-binding transcriptional repressor

Synonyms: PurR-hypoxanthine

Subunit composition of PurR-Hypoxanthine DNA-binding transcriptional repressor = [(PurR)2][hypoxanthine]
         PurR transcriptional repressor = (PurR)2 (extended summary available)

Citations: [FukamiKobayashi03, Rolfes88, Choi90, He92]

Sequence Length: 341 AAs

In Reactions of unknown directionality:

Not in pathways:
PurR + hypoxanthine = PurR-hypoxanthine

MultiFun Terms: extrachromosomal colicin related
information transfer RNA related Transcription related
metabolism biosynthesis of building blocks amino acids histidine
metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone
metabolism biosynthesis of building blocks nucleotides purine biosynthesis
metabolism biosynthesis of building blocks nucleotides pyrimidine biosynthesis
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
metabolism central intermediary metabolism nucleotide and nucleoside conversions
metabolism central intermediary metabolism polyamine biosynthesis
metabolism metabolism of other compounds nitrogen metabolism
regulation genetic unit regulated regulon
regulation
regulation type of regulation transcriptional level repressor

DNA binding site length: 16 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: ACGCAAACGTTTGCGT

Regulated Transcription Units (20 total): ?

Notes:


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Rolfes90a, UniProt11]
UniProt: Removed.
Conserved-Region 2 -> 56
[UniProt09]
UniProt: HTH lacI-type;
Chain 2 -> 341
[UniProt09]
UniProt: HTH-type transcriptional repressor purR;
DNA-Binding-Region 4 -> 23
[UniProt10a]
UniProt: H-T-H motif;
DNA-Binding-Region 48 -> 56
[UniProt10a]
Mutagenesis-Variant 54
[UniProt10a]
Alternate sequence: L → M; UniProt: Slight decrease in operator DNA affinity;
Mutagenesis-Variant 55
[Glasfeld99, UniProt11]
Alternate sequence: K → A; UniProt: Decrease in operator DNA affinity.
Amino-Acid-Sites-That-Bind 73
[UniProt10a]
UniProt: Corepressor;
Mutagenesis-Variant 147
[Huffman02, UniProt11]
Alternate sequence: W → R; UniProt: 8-fold increase in corepressor affinity. Large increase in repressor activity.
Alternate sequence: W → F; UniProt: Large decrease in corepressor affinity and in repressor activity.
Alternate sequence: W → A; UniProt: 14-fold increase in corepressor affinity. Large increase in repressor activity.
Mutagenesis-Variant 190
[Lu98, UniProt11]
Alternate sequence: R → Q; UniProt: Functional repressor. Corepressor specificity is expanded since it allows binding of adenine.
Alternate sequence: R → A; UniProt: Functional repressor. Corepressor specificity is expanded since it allows binding of adenine and 6-methylpurine.
Amino-Acid-Sites-That-Bind 190
[UniProt10a]
UniProt: Corepressor;
Amino-Acid-Sites-That-Bind 192
[UniProt10a]
UniProt: Corepressor;
Amino-Acid-Sites-That-Bind 221
[UniProt10a]
UniProt: Corepressor;
Amino-Acid-Sites-That-Bind 275
[UniProt10a]
UniProt: Corepressor;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b1658 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10800; confirmed by SwissProt match.


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

Cho11: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102

Choi90: Choi KY, Zalkin H (1990). "Regulation of Escherichia coli pyrC by the purine regulon repressor protein." J Bacteriol 172(6);3201-7. PMID: 1971620

Choi92: Choi KY, Zalkin H (1992). "Structural characterization and corepressor binding of the Escherichia coli purine repressor." J Bacteriol 174(19);6207-14. PMID: 1400170

Choi94: Choi KY, Zalkin H (1994). "Role of the purine repressor hinge sequence in repressor function." J Bacteriol 176(6);1767-72. PMID: 8132474

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

FukamiKobayashi03: Fukami-Kobayashi K, Tateno Y, Nishikawa K (2003). "Parallel evolution of ligand specificity between LacI/GalR family repressors and periplasmic sugar-binding proteins." Mol Biol Evol 20(2);267-77. PMID: 12598694

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

Glasfeld99: Glasfeld A, Koehler AN, Schumacher MA, Brennan RG (1999). "The role of lysine 55 in determining the specificity of the purine repressor for its operators through minor groove interactions." J Mol Biol 291(2);347-61. PMID: 10438625

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

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

He90: He B, Shiau A, Choi KY, Zalkin H, Smith JM (1990). "Genes of the Escherichia coli pur regulon are negatively controlled by a repressor-operator interaction." J Bacteriol 1990;172(8);4555-62. PMID: 2198266

He92: He B, Smith JM, Zalkin H (1992). "Escherichia coli purB gene: cloning, nucleotide sequence, and regulation by purR." J Bacteriol 1992;174(1);130-6. PMID: 1729205

He94: He B, Zalkin H (1994). "Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism." J Bacteriol 176(4);1009-13. PMID: 8106311

Huffman02: Huffman JL, Lu F, Zalkin H, Brennan RG (2002). "Role of residue 147 in the gene regulatory function of the Escherichia coli purine repressor." Biochemistry 41(2);511-20. PMID: 11781089

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lu98: Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG (1998). "Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190." Biochemistry 37(4);971-82. PMID: 9454587

Meng90: Meng LM, Kilstrup M, Nygaard P (1990). "Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli." Eur J Biochem 1990;187(2);373-9. PMID: 2404765

Meng90a: Meng LM, Nygaard P (1990). "Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli." Mol Microbiol 4(12);2187-92. PMID: 2089227

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

Rolfes88: Rolfes RJ, Zalkin H (1988). "Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator." J Biol Chem 263(36);19653-61. PMID: 3058704

Rolfes90: Rolfes RJ, Zalkin H (1990). "Autoregulation of Escherichia coli purR requires two control sites downstream of the promoter." J Bacteriol 172(10);5758-66. PMID: 2211510

Rolfes90a: Rolfes RJ, Zalkin H (1990). "Purification of the Escherichia coli purine regulon repressor and identification of corepressors." J Bacteriol 172(10);5637-42. PMID: 2211500

Schumacher93: Schumacher MA, Macdonald JR, Bjorkman J, Mowbray SL, Brennan RG (1993). "Structural analysis of the purine repressor, an Escherichia coli DNA-binding protein." J Biol Chem 268(17);12282-8. PMID: 8509365

SwintKruse02: Swint-Kruse L, Larson C, Pettitt BM, Matthews KS (2002). "Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR." Protein Sci 11(4);778-94. PMID: 11910022

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

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

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Other References Related to Gene Regulation

Stojiljkovic94: Stojiljkovic I, Baumler AJ, Hantke K (1994). "Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay." J Mol Biol 236(2);531-45. PMID: 8107138


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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