Escherichia coli K-12 substr. MG1655 Enzyme: pyrimidine nucleotidase

Gene: yjjG Accession Numbers: EG12115 (EcoCyc), b4374, ECK4365

Regulation Summary Diagram: ?

Regulation summary diagram for yjjG

YjjG is a monophosphatase whose activity is essential for thymine salvage in a thyA (thymidylate synthase) mutant. The dUMP phosphatase activity of YjjG generates deoxyuridine, which can be used by DeoA to liberate the deoxyribose-1-phosphate required for salvage of thymine [Weiss07, Itsko11].

YjjG was first identified as a pyrimidine nucleotidase belonging to the superfamily of haloacid dehalogenase (HAD)-like hydrolases. YjjG has phosphatase activity towards UMP, dUMP, and dTMP, and the activity is inhibited by nucleoside di- and triphosphates [Proudfoot04, Kuznetsova06]. The enzyme shows a low level of substrate discrimination among its preferred substrates [Kuznetsova06]. The phosphatase activity of YjjG was also shown in a high-throughput screen of purified proteins [Kuznetsova05].

The general nucleotidase activity of YjjG allows it to protect cells against the potentially mutagenic noncanonical pyrimidine nucleotides, preventing their incorporation into DNA [Titz07].

YjjG is oligomeric in solution [Proudfoot04].

The enzyme is likely identical to a partially purified 5'-nucleotidase from E. coli B [Uerkvitz73].

A yjjG thyA double mutant is unable to use thymine for growth on glucose minimal medium [Weiss07]. A yjjG mutant is sensitive to toxic noncanonical pyrimidine derivatives such as 5-fluorodeoxyuridine [Titz07].

Locations: cytosol

Map Position: [4,606,669 -> 4,607,346] (99.29 centisomes, 357°)
Length: 678 bp / 225 aa

Molecular Weight of Polypeptide: 25.301 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014344 , EchoBASE:EB2038 , EcoGene:EG12115 , EcoliWiki:b4374 , ModBase:P0A8Y1 , OU-Microarray:b4374 , PortEco:yjjG , Pride:P0A8Y1 , Protein Model Portal:P0A8Y1 , RefSeq:NP_418791 , RegulonDB:EG12115 , SMR:P0A8Y1 , String:511145.b4374 , Swiss-Model:P0A8Y1 , UniProt:P0A8Y1

Relationship Links: InterPro:IN-FAMILY:IPR006439 , InterPro:IN-FAMILY:IPR011951 , InterPro:IN-FAMILY:IPR023198 , InterPro:IN-FAMILY:IPR023214 , Pfam:IN-FAMILY:PF00702

In Paralogous Gene Group: 276 (8 members) , 525 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Instance reaction of [a nucleoside 5'-monophosphate[periplasmic space] + H2O[periplasmic space] → a nucleoside[periplasmic space] + phosphate[periplasmic space]] (no EC#):
i1: a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate (

Instance reactions of [a ribonucleoside 5'-monophosphate + H2O → a ribonucleoside + phosphate] (
i2: CMP + H2O → cytidine + phosphate (

i3: UMP + H2O → uridine + phosphate (

i4: AMP + H2O → adenosine + phosphate (

GO Terms:

Biological Process: GO:0009410 - response to xenobiotic stimulus Inferred from experiment [Titz07]
GO:0016311 - dephosphorylation Inferred from experiment Inferred by computational analysis [GOA01a, Kuznetsova06, Proudfoot04]
GO:0019859 - thymine metabolic process Inferred from experiment [Weiss07]
GO:0043100 - pyrimidine nucleobase salvage Inferred from experiment [Weiss07]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0008253 - 5'-nucleotidase activity Inferred from experiment Inferred by computational analysis [GOA01a, Kuznetsova06]
GO:0016791 - phosphatase activity Inferred from experiment [Proudfoot04]
GO:0030145 - manganese ion binding Inferred from experiment [Kuznetsova06]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection detoxification
metabolism biosynthesis of building blocks nucleotides

Essentiality data for yjjG 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]
Yes [Feist07, Comment 4]

Last-Curated ? 13-Jul-2011 by Keseler I , SRI International

Enzymatic reaction of: pyrimidine nucleotidase

Synonyms: HAD5

EC Number:

a ribonucleoside 5'-monophosphate + H2O <=> a ribonucleoside + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for a ribonucleoside 5'-monophosphate: imidodiphosphate [Kuznetsova06 ] , dUMP [Proudfoot04 ] , dTMP [Proudfoot04 ] , UMP [Proudfoot04 ]

Cofactors or Prosthetic Groups: Mn2+ [Kuznetsova06, Proudfoot04]

pH(opt): 7 [BRENDA14, Proudfoot04], 8 [BRENDA14, Proudfoot04], 7.5 [Proudfoot04]

Sequence Features

Protein sequence of pyrimidine nucleotidase with features indicated

Feature Class Location Citations Comment
Active-Site 9
UniProt: Nucleophile; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 75
[Grentzmann93, UniProt15]
UniProt: (in Ref. 2).
Sequence-Conflict 100
[Grentzmann93, UniProt15]
UniProt: (in Ref. 2).
Sequence-Conflict 130
[Grentzmann93, UniProt15]
UniProt: (in Ref. 2).

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b4374 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12115; confirmed by SwissProt match.


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

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

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

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.

Grentzmann93: Grentzmann G., Brechemier-Baey D., Heurgue V., Mora L., Buckingham R.H. (1993). Data submission to EMBL/GenBank/DDBJ databases on 1993-09.

Itsko11: Itsko M, Schaaper RM (2011). "The dgt gene of Escherichia coli facilitates thymine utilization in thymine-requiring strains." Mol Microbiol 81(5);1221-32. PMID: 21736641

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

Kuznetsova05: Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF (2005). "Enzyme genomics: Application of general enzymatic screens to discover new enzymes." FEMS Microbiol Rev 29(2);263-79. PMID: 15808744

Kuznetsova06: Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF (2006). "Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family." J Biol Chem 281(47):36149-61. PMID: 16990279

Proudfoot04: Proudfoot M, Kuznetsova E, Brown G, Rao NN, Kitagawa M, Mori H, Savchenko A, Yakunin AF (2004). "General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG." J Biol Chem 279(52);54687-94. PMID: 15489502

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Titz07: Titz B, Hauser R, Engelbrecher A, Uetz P (2007). "The Escherichia coli protein YjjG is a house-cleaning nucleotidase in vivo." FEMS Microbiol Lett 270(1);49-57. PMID: 17286574

Uerkvitz73: Uerkvitz W, Karlstrom O, Munch-Petersen A (1973). "A deoxyuridine monophosphate phosphatase detected in mutants of Escherichia coli lacking alkaline phosphatase and 5'-nucleotidase." Mol Gen Genet 121(4);337-46. PMID: 4571806

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.

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

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

Weiss07: Weiss B (2007). "YjjG, a dUMP phosphatase, is critical for thymine utilization by Escherichia coli K-12." J Bacteriol 189(5);2186-9. PMID: 17189366

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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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 Tue Oct 6, 2015, biocyc13.