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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Enzyme: pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase

Gene: nudI Accession Numbers: G7164 (MetaCyc), b2251, ECK2244

Synonyms: yfaO

Species: Escherichia coli K-12 substr. MG1655

Summary:
The nudI gene product is a member of the Nudix hydrolase superfamily of nucleoside diphosphatases. The preferred substrate of the purified enzyme is dUTP, but it also shows 67 and 58% of activity with dTTP and dCTP, respectively. The enzyme is a monomer in solution [Xu06b].

Review: [McLennan06]

The crystal structure of the Nudix hydrolase product of Orf141 from Escherichia coli strain K-1 has been determined. This enzyme cleaves pyrimidine deoxynucleoside triphosphates [Jung07].

Locations: cytosol

Map Position: [2,362,576 -> 2,363,001]

Molecular Weight of Polypeptide: 16.371 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007449 , DIP:DIP-11948N , EchoBASE:EB3060 , EcoGene:EG13275 , EcoliWiki:b2251 , Mint:MINT-1262923 , ModBase:P52006 , OU-Microarray:b2251 , PortEco:nudI , PR:PRO_000023426 , Protein Model Portal:P52006 , RefSeq:NP_416754 , RegulonDB:G7164 , SMR:P52006 , String:511145.b2251 , UniProt:P52006

Relationship Links: InterPro:IN-FAMILY:IPR000086 , InterPro:IN-FAMILY:IPR015797 , InterPro:IN-FAMILY:IPR020084 , InterPro:IN-FAMILY:IPR020476 , InterPro:IN-FAMILY:IPR023781 , Pfam:IN-FAMILY:PF00293 , Prints:IN-FAMILY:PR00502 , Prosite:IN-FAMILY:PS00893 , Prosite:IN-FAMILY:PS51462

Gene-Reaction Schematic: ?

Instance reactions of [a nucleoside triphosphate + H2O → a nucleoside 5'-monophosphate + diphosphate + H+] (3.6.1.19):
i1: CTP + H2O → CMP + diphosphate + H+ (3.6.1.19/3.6.1.65)

i2: dCTP + H2O → dCMP + diphosphate + H+ (3.6.1.12/3.6.1.19/3.6.1.65)

i3: dUTP + H2O → dUMP + diphosphate + H+ (3.6.1.19/3.6.1.23)

i4: dTTP + H2O → dTMP + diphosphate + H+ (3.6.1.19)

i5: dATP + H2O → dAMP + diphosphate + H+ (3.6.1.19)

i6: UTP + H2O → UMP + diphosphate + H+ (3.6.1.19)

i7: dGTP + H2O → dGMP + diphosphate + H+ (3.6.1.19)

i8: dITP + H2O → dIMP + diphosphate + H+ (3.6.1.66)

i9: GTP + H2O → GMP + diphosphate + H+ (3.6.1.19)

i10: ITP + H2O → IMP + diphosphate + H+ (3.6.1.19)

i11: ATP + H2O → AMP + diphosphate + H+ (3.6.1.8)

i12: XTP + H2O → XMP + diphosphate + H+ (3.6.1.66)

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Xu06b, UniProtGOA11a, GOA06, GOA01a]
Molecular Function: GO:0004170 - dUTP diphosphatase activity Inferred from experiment [Xu06b]
GO:0047840 - dCTP diphosphatase activity Inferred from experiment [Xu06b]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides Inferred by computational analysis [GOA01a]
GO:0050355 - triphosphatase activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: dUTP pyrophosphohydrolase (pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase)

EC Number: 3.6.1.23

dUTP + H2O <=> dUMP + diphosphate + H+

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 physiologically favored in the direction shown.

In Pathways: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) , superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis , pyrimidine deoxyribonucleotides de novo biosynthesis II , pyrimidine deoxyribonucleotides de novo biosynthesis I , pyrimidine deoxyribonucleotides dephosphorylation

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Kinetic Parameters:

Substrate
Km (μM)
Citations
dUTP
2200.0
[Xu06b]


Enzymatic reaction of: dCTP pyrophosphohydrolase (pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase)

EC Number: 3.6.1.12

dCTP + H2O <=> dCMP + diphosphate + H+

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 physiologically favored in the direction shown.

Alternative Substrates for dCTP: dCDP [Xu06b ]

In Pathways: pyrimidine deoxyribonucleotides dephosphorylation

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: dTTP pyrophosphohydrolase (pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase)

dTTP + H2O <=> dTMP + diphosphate + H+

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 physiologically favored in the direction shown.

Alternative Substrates for dTTP: dTDP [Xu06b ]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Kinetic Parameters:

Substrate
Km (μM)
Citations
dTTP
1300.0
[Xu06b]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 141
[UniProt09]
UniProt: Nudix hydrolase;
Protein-Segment 38 -> 59
[UniProt10]
UniProt: Nudix box; Sequence Annotation Type: short sequence motif;

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


References

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

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."

Jung07: Jung J, Ahn YJ, Kang LW (2007). "Overexpression, crystallization and preliminary X-ray crystallographic analysis of Nudix hydrolase Orf141 from Escherichia coli K-1." Acta Crystallogr Sect F Struct Biol Cryst Commun 63(Pt 9);812-5. PMID: 17768363

McLennan06: McLennan AG (2006). "The Nudix hydrolase superfamily." Cell Mol Life Sci 63(2);123-43. PMID: 16378245

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

Xu06b: Xu W, Dunn CA, O'handley SF, Smith DL, Bessman MJ (2006). "Three new Nudix hydrolases from Escherichia coli." J Biol Chem 281(32);22794-8. PMID: 16766526


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, BIOCYC14B.