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Escherichia coli K-12 substr. MG1655 Enzyme: orotate phosphoribosyltransferase



Gene: pyrE Accession Numbers: EG10808 (EcoCyc), b3642, ECK3632

Regulation Summary Diagram: ?

Subunit composition of orotate phosphoribosyltransferase = [PyrE]2

Summary:
Orotate phosphoribosyltransferase (PyrE) catalyzes the transfer of the phosphoribosyl moiety to the pyrimidine ring in the de novo biosynthesis of pyrimidine nucleotides.

A crystal structure of PyrE has been solved [Aghajari94, Henriksen96].

Expression of PyrE is regulated in response to UTP levels by transcriptional attenuation at a terminator structure between the rph and pyrE genes in the rph-pyrE operon [Poulsen84, Bonekamp84, Poulsen87]. Efficient translation of the upstream ORF also leads to higher PyrE expression [Bonekamp84, Bonekamp85, Poulsen87], and inefficient translation leads to enhanced regulation of PyrE expression by the UTP pool [Jensen88]. Coupling between transcription and translation is required for proper regulation of PyrE expression [Andersen91]. Low levels of PyrE are found in E. coli strain W1485 and its daughters W3110 and MG1655 because of a frame shift mutation in rph, affecting transcription of pyrE [Jensen93]. An 82 bp deletion in the rph-pyrE operon was found in the majority of cultures that had undergone laboratory evolution and may relieve the defect in pyrimidine biosynthesis of the MG1655 parent [Conrad09].

Review: [Turnbough08]

Gene Citations: [Andersen92]

Locations: cytosol

Map Position: [3,813,150 <- 3,813,791] (82.19 centisomes)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 23.567 kD (from nucleotide sequence), 23.0 kD (experimental) [Poulsen83 ]

Molecular Weight of Multimer: 47.0 kD (experimental) [Shimosaka85]

pI: 5.54

Unification Links: ASAP:ABE-0011904 , CGSC:327 , EchoBASE:EB0801 , EcoGene:EG10808 , EcoliWiki:b3642 , OU-Microarray:b3642 , PortEco:pyrE , PR:PRO_000023660 , Pride:P0A7E3 , Protein Model Portal:P0A7E3 , RefSeq:NP_418099 , RegulonDB:EG10808 , SMR:P0A7E3 , String:511145.b3642 , UniProt:P0A7E3

Relationship Links: InterPro:IN-FAMILY:IPR000836 , InterPro:IN-FAMILY:IPR004467 , InterPro:IN-FAMILY:IPR023031 , PDB:Structure:1ORO , Pfam:IN-FAMILY:PF00156 , Prosite:IN-FAMILY:PS00103

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006207 - 'de novo' pyrimidine nucleobase biosynthetic process Inferred from experiment [Jensen93]
GO:0006221 - pyrimidine nucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Jensen93]
GO:0009116 - nucleoside metabolic process Inferred by computational analysis [GOA01]
GO:0044205 - 'de novo' UMP biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment Inferred by computational analysis [GOA06, Dodin82, Shimosaka85, Henriksen96]
GO:0004588 - orotate phosphoribosyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Dodin81]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016757 - transferase activity, transferring glycosyl groups Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Dodin81]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides pyrimidine biosynthesis

Essentiality data for pyrE 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Credits:
Last-Curated ? 14-Jul-2010 by Keseler I , SRI International


Enzymatic reaction of: orotate phosphoribosyltransferase

Synonyms: orotidylic acid phosphorylase, orotidine-5'-phosphate pyrophosphorylase, orotidine-5'-phosphate:pyrophosphate phospho-α-D-ribosyl-transferase

EC Number: 2.4.2.10

orotidine 5'-phosphate + diphosphate <=> 5-phospho-α-D-ribose 1-diphosphate + orotate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Shimosaka85]

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis , superpathway of pyrimidine ribonucleotides de novo biosynthesis , UMP biosynthesis

Cofactors or Prosthetic Groups: Mg2+ [Shimosaka85]

Kinetic Parameters:

Substrate
Km (μM)
Citations
orotidine 5'-phosphate
3.1, 3.6
[Shimosaka85, BRENDA14]
orotate
30.0
[Shimosaka85, BRENDA14]
diphosphate
220.0, 13.0
[Shimosaka85, BRENDA14]
5-phospho-α-D-ribose 1-diphosphate
38.0, 40.0
[Shimosaka85, BRENDA14]

pH(opt): 9.5 [Shimosaka85]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10a]
UniProt: Removed;
Chain 2 -> 213
[UniProt09]
UniProt: Orotate phosphoribosyltransferase;
Amino-Acid-Sites-That-Bind 26
[UniProt10]
UniProt: 5-phosphoribose 1-diphosphate; Non-Experimental Qualifier: by similarity;
Protein-Segment 34 -> 35
[UniProt10]
UniProt: Orotate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Protein-Segment 72 -> 73
[UniProt10]
UniProt: 5-phosphoribose 1-diphosphate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 99
[UniProt10a]
UniProt: 5-phosphoribose 1-diphosphate; shared with dimeric partner;
Amino-Acid-Sites-That-Bind 100
[UniProt10a]
UniProt: 5-phosphoribose 1-diphosphate;
Amino-Acid-Sites-That-Bind 103
[UniProt10a]
UniProt: 5-phosphoribose 1-diphosphate; shared with dimeric partner;
Amino-Acid-Sites-That-Bind 105
[UniProt10]
UniProt: 5-phosphoribose 1-diphosphate; shared with dimeric partner; Non-Experimental Qualifier: by similarity;
Protein-Segment 124 -> 132
[UniProt10]
UniProt: 5-phosphoribose 1-diphosphate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 128
[UniProt10]
UniProt: Orotate; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 133
[Poulsen84, Poulsen83, UniProt10a]
Alternate sequence: I → missing; UniProt: (in Ref. 1 and 2);
Amino-Acid-Sites-That-Bind 156
[UniProt10]
UniProt: Orotate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3642 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10808.


References

Aghajari94: Aghajari N, Jensen KF, Gajhede M (1994). "Crystallization and preliminary X-ray diffraction studies on the Apo form of orotate phosphoribosyltransferase from Escherichia coli." J Mol Biol 241(2);292-4. PMID: 8057372

Andersen91: Andersen JT, Jensen KF, Poulsen P (1991). "Role of transcription pausing in the control of the pyrE attenuator in Escherichia coli." Mol Microbiol 5(2);327-33. PMID: 1710313

Andersen92: Andersen JT, Poulsen P, Jensen KF (1992). "Attenuation in the rph-pyrE operon of Escherichia coli and processing of the dicistronic mRNA." Eur J Biochem 206(2);381-90. PMID: 1375912

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

Bonekamp84: Bonekamp F, Clemmesen K, Karlstrom O, Jensen KF (1984). "Mechanism of UTP-modulated attenuation at the pyrE gene of Escherichia coli: an example of operon polarity control through the coupling of translation to transcription." EMBO J 3(12);2857-61. PMID: 6098450

Bonekamp85: Bonekamp F, Andersen HD, Christensen T, Jensen KF (1985). "Codon-defined ribosomal pausing in Escherichia coli detected by using the pyrE attenuator to probe the coupling between transcription and translation." Nucleic Acids Res 13(11);4113-23. PMID: 2989788

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Christopherson78: Christopherson RI, Finch LR (1978). "Response of the pyrimidine pathway of Escherichia coli K 12 to exogenous adenine and uracil." Eur J Biochem 90(2);347-58. PMID: 361403

Conrad09: Conrad TM, Joyce AR, Applebee MK, Barrett CL, Xie B, Gao Y, Palsson BO (2009). "Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations." Genome Biol 10(10);R118. PMID: 19849850

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

Dodin81: Dodin G (1981). "A rapid purification by affinity chromatography of orotate phosphoribosyltransferase from Escherichia coli K-12." FEBS Lett 134(1);20-4. PMID: 9222315

Dodin82: Dodin G, Lalart D, Dubois JE (1982). "Role of magnesium cations in the yeast orotate phosphoribosyltransferase catalyzed reaction. Mechanism of the inhibition by Cu++ and Ni++ ions." J Inorg Biochem 16(3);201-13. PMID: 7050303

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Henriksen96: Henriksen A, Aghajari N, Jensen KF, Gajhede M (1996). "A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase." Biochemistry 35(12);3803-9. PMID: 8620002

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

Jensen88: Jensen KF (1988). "Hyper-regulation of pyr gene expression in Escherichia coli cells with slow ribosomes. Evidence for RNA polymerase pausing in vivo?." Eur J Biochem 175(3);587-93. PMID: 3044790

Jensen93: Jensen KF (1993). "The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels." J Bacteriol 1993;175(11);3401-7. PMID: 8501045

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

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Poulsen83: Poulsen P, Jensen KF, Valentin-Hansen P, Carlsson P, Lundberg LG (1983). "Nucleotide sequence of the Escherichia coli pyrE gene and of the DNA in front of the protein-coding region." Eur J Biochem 135(2);223-9. PMID: 6349999

Poulsen84: Poulsen P, Bonekamp F, Jensen KF (1984). "Structure of the Escherichia coli pyrE operon and control of pyrE expression by a UTP modulated intercistronic attentuation." EMBO J 1984;3(8);1783-90. PMID: 6207018

Poulsen87: Poulsen P, Jensen KF (1987). "Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli." Mol Gen Genet 208(1-2);152-8. PMID: 3302606

Shimosaka84: Shimosaka M, Fukuda Y, Murata K, Kimura A (1984). "Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12." J Bacteriol 160(3);1101-4. PMID: 6389507

Shimosaka85: Shimosaka M, Fukuda Y, Murata K, Kimura A (1985). "Purification and properties of orotate phosphoribosyltransferases from Escherichia coli K-12, and its derivative purine-sensitive mutant." J Biochem 98(6);1689-97. PMID: 2419315

Turnbough08: Turnbough CL, Switzer RL (2008). "Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors." Microbiol Mol Biol Rev 72(2);266-300, table of contents. PMID: 18535147

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.

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."


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 Dec 18, 2014, biocyc13.