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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
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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 [Xu06e].

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 [Xu06e, UniProtGOA11a, GOA06, GOA01a]
Molecular Function: GO:0004170 - dUTP diphosphatase activity Inferred from experiment [Xu06e]
GO:0047840 - dCTP diphosphatase activity Inferred from experiment [Xu06e]
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
[Xu06e]


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 [Xu06e ]

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 [Xu06e ]

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

Kinetic Parameters:

Substrate
Km (μM)
Citations
dTTP
1300.0
[Xu06e]


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 1 -> 141
[UniProt09]
UniProt: Nudix hydrolase;
Protein-Segment 38 -> 59
[UniProt10a]
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.

UniProt10a: 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."

Xu06e: 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 Mon Dec 22, 2014, BIOCYC13B.