Escherichia coli K-12 substr. MG1655 Enzyme: orotidine-5'-phosphate decarboxylase

Gene: pyrF Accession Numbers: EG10809 (EcoCyc), b1281, ECK1276

Regulation Summary Diagram: ?

Regulation summary diagram for pyrF

Subunit composition of orotidine-5'-phosphate decarboxylase = [PyrF]2

Orotidine-5'-phosphate-decarboxylase (PyrF) catalyzes the last essential step in the de novo biosynthesis of pyrimidines, the synthesis of UMP by decarboxylation of orotidine-5'-phosphate. The enzyme is extremely proficient; the non-enzymatic rate of OMP decarboxylation at room temperature is extremely low at 2.8 x 10-16 s-1 [Radzicka95]. PyrF enhances the reaction rate by a factor of 1017, and the catalytic mechanism underlying this high efficiency has been the subject of investigation and debate [Wepukhulu08].

PyrF is a dimer in solution [Donovan83]. Crystal structures of the enzyme have been solved [Harris00, Poulsen01, Harris02]. Computational simulations of proposed reaction mechanisms have been performed [Raugei04, Stanton07].

pyrF mutants excrete orotic acid under conditions when normal strains excrete uracil [Womack78]. Strains deficient in polynucleotide phosphorylase show higher PyrF activity than wild-type strains [Donovan83a].

Reviews: [Begley00, Miller02a, Gao03a, Callahan07]

Gene Citations: [Nonaka06]

Locations: cytosol

Map Position: [1,339,945 -> 1,340,682] (28.88 centisomes, 104°)
Length: 738 bp / 245 aa

Molecular Weight of Polypeptide: 26.35 kD (from nucleotide sequence), 27 kD (experimental) [Donovan83 ]

Molecular Weight of Multimer: 54.0 kD (experimental) [Donovan83]

Unification Links: ASAP:ABE-0004304 , CGSC:326 , EchoBASE:EB0802 , EcoGene:EG10809 , EcoliWiki:b1281 , ModBase:P08244 , OU-Microarray:b1281 , PortEco:pyrF , PR:PRO_000023661 , Pride:P08244 , Protein Model Portal:P08244 , RefSeq:NP_415797 , RegulonDB:EG10809 , SMR:P08244 , String:511145.b1281 , UniProt:P08244

Relationship Links: InterPro:IN-FAMILY:IPR001754 , InterPro:IN-FAMILY:IPR011060 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR014732 , InterPro:IN-FAMILY:IPR018089 , PDB:Structure:1EIX , PDB:Structure:1JJK , PDB:Structure:1L2U , Pfam:IN-FAMILY:PF00215 , Prosite:IN-FAMILY:PS00156 , Smart:IN-FAMILY:SM00934

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006207 - 'de novo' pyrimidine nucleobase biosynthetic process Inferred from experiment Inferred by computational analysis [GOA01a, Jensen84]
GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Donovan83]
GO:0006221 - pyrimidine nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0006222 - UMP biosynthetic process Inferred by computational analysis [Gaudet10]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0044205 - 'de novo' UMP biosynthetic process Inferred by computational analysis [UniProtGOA12, GOA01a]
Molecular Function: GO:0004590 - orotidine-5'-phosphate decarboxylase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Donovan83]
GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06]
GO:0016831 - carboxy-lyase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Donovan83]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Donovan83]
GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [Gaudet10, DiazMejia09, Ishihama08, LopezCampistrou05]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides pyrimidine biosynthesis
metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for pyrF 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 2]
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 1]
No [Feist07, Comment 3]

Curated 13-Mar-2006 by Shearer A , SRI International
Last-Curated ? 14-Jul-2010 by Keseler I , SRI International

Enzymatic reaction of: orotidine-5'-phosphate decarboxylase

Synonyms: orotidylic decarboxylase, OMP decarboxylase, orotidine-5'-phosphate carboxy-lyase, ODCase

EC Number:

orotidine 5'-phosphate + H+ <=> CO2 + UMP

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

The reaction is irreversible in the direction shown.

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

Inhibitors (Competitive): 6-phosphonouridine 5'-monophosphate [Thirumalairajan10]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
orotidine 5'-phosphate
[Donovan83, BRENDA14]
orotidine 5'-phosphate
[Harris00, BRENDA14]

T(opt): 25 °C [BRENDA14, Wepukhulu08]

pH(opt): 7 [BRENDA14, Wepukhulu08]

Sequence Features

Protein sequence of PyrF with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
Amino-Acid-Sites-That-Bind 22
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 44
UniProt: Substrate.
Protein-Segment 71 -> 80
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Active-Site 73
UniProt: Proton donor.
Amino-Acid-Sites-That-Bind 131
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 192
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 201
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 221
UniProt: Substrate; via amide nitrogen.
Amino-Acid-Sites-That-Bind 222
UniProt: Substrate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1281 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10809; confirmed by SwissProt match.


Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Begley00: Begley TP, Appleby TC, Ealick SE (2000). "The structural basis for the remarkable catalytic proficiency of orotidine 5'-monophosphate decarboxylase." Curr Opin Struct Biol 10(6);711-8. PMID: 11114509

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

Callahan07: Callahan BP, Miller BG (2007). "OMP decarboxylase--An enigma persists." Bioorg Chem 35(6);465-9. PMID: 17889251

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

Donovan83: Donovan WP, Kushner SR (1983). "Purification and characterization of orotidine-5'-phosphate decarboxylase from Escherichia coli K-12." J Bacteriol 1983;156(2);620-4. PMID: 6355062

Donovan83a: Donovan WP, Kushner SR (1983). "Cloning and physical analysis of the pyrF gene (coding for orotidine-5'-phosphate decarboxylase) from Escherichia coli K-12." Gene 1983;25(1);39-48. PMID: 6319231

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

Gao03a: Gao J (2003). "Catalysis by enzyme conformational change as illustrated by orotidine 5'-monophosphate decarboxylase." Curr Opin Struct Biol 13(2);184-92. PMID: 12727511

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: 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."

Harris00: Harris P, Navarro Poulsen JC, Jensen KF, Larsen S (2000). "Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase." Biochemistry 39(15);4217-24. PMID: 10757968

Harris02: Harris P, Poulsen JC, Jensen KF, Larsen S (2002). "Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase." J Mol Biol 318(4);1019-29. PMID: 12054799

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

Jensen84: Jensen KF, Larsen JN, Schack L, Sivertsen A (1984). "Studies on the structure and expression of Escherichia coli pyrC, pyrD, and pyrF using the cloned genes." Eur J Biochem 140(2);343-52. PMID: 6370696

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

Miller02a: Miller BG, Wolfenden R (2002). "Catalytic proficiency: the unusual case of OMP decarboxylase." Annu Rev Biochem 71;847-85. PMID: 12045113

Nonaka06: Nonaka G, Blankschien M, Herman C, Gross CA, Rhodius VA (2006). "Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress." Genes Dev 20(13);1776-89. PMID: 16818608

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

Poulsen01: Poulsen JC, Harris P, Jensen KF, Larsen S (2001). "Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group." Acta Crystallogr D Biol Crystallogr 57(Pt 9);1251-9. PMID: 11526316

Radzicka95: Radzicka A, Wolfenden R (1995). "A proficient enzyme." Science 267(5194);90-3. PMID: 7809611

Raugei04: Raugei S, Cascella M, Carloni P (2004). "A proficient enzyme: insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations." J Am Chem Soc 126(48);15730-7. PMID: 15571395

Stanton07: Stanton CL, Kuo IF, Mundy CJ, Laino T, Houk KN (2007). "QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5'-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis." J Phys Chem B 111(43);12573-81. PMID: 17927240

Thirumalairajan10: Thirumalairajan S, Mahaney B, Bearne SL (2010). "Interrogation of the active site of OMP decarboxylase from Escherichia coli with a substrate analogue bearing an anionic group at C6." Chem Commun (Camb) 46(18);3158-60. PMID: 20424759

Turnbough87: Turnbough CL, Kerr KH, Funderburg WR, Donahue JP, Powell FE (1987). "Nucleotide sequence and characterization of the pyrF operon of Escherichia coli K12." J Biol Chem 1987;262(21);10239-45. PMID: 2956254

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: 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."

Wepukhulu08: Wepukhulu WO, Smiley VL, Vemulapalli B, Smiley JA, Phillips LM, Lee JK (2008). "A substantial oxygen isotope effect at O2 in the OMP decarboxylase reaction: mechanistic implications." Org Biomol Chem 6(24);4533-41. PMID: 19039361

Womack78: Womack JE, O'Donovan GA (1978). "Orotic acid excretion in some wild-type strains of Escherichia coli K-12." J Bacteriol 136(2);825-7. PMID: 361725

Other References Related to Gene Regulation

Klein14: Klein G, Kobylak N, Lindner B, Stupak A, Raina S (2014). "Assembly of lipopolysaccharide in Escherichia coli requires the essential LapB heat shock protein." J Biol Chem 289(21);14829-53. PMID: 24722986

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065

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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 Sat Oct 10, 2015, biocyc13.