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Escherichia coli K-12 substr. MG1655 Enzyme: pyrimidine deoxynucleoside triphosphate pyrophosphohydrolase



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

Synonyms: yfaO

Regulation Summary Diagram: ?

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] (50.92 centisomes)
Length: 426 bp / 141 aa

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

In Paralogous Gene Group: 33 (6 members)

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+ (3.6.1.65)

i2: dATP + H2O → dAMP + diphosphate + H+ (3.6.1.19)

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

i4: dGTP + H2O → dGMP + diphosphate + H+ (3.6.1.19)

i5: dITP + H2O → dIMP + diphosphate + H+ (3.6.1.66)

i6: ITP + H2O → IMP + diphosphate + H+ (3.6.1.19)

i7: XTP + H2O → XMP + diphosphate + H+ (3.6.1.66)

i8: ATP + H2O → AMP + diphosphate + H+ (3.6.1.8)

i9: dTTP + H2O → dTMP + diphosphate + H+ (3.6.1.19)

i10: UTP + H2O → UMP + diphosphate + H+ (3.6.1.19)

i11: dCTP + H2O → dCMP + diphosphate + H+ (3.6.1.12/3.6.1.19/3.6.1.65)

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis Inferred from experiment [Xu06b, UniProtGOA11, GOA06, GOA01]
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 [UniProtGOA11, GOA01]
GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides Inferred by computational analysis [GOA01]
GO:0050355 - triphosphatase activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for nudI 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]

Credits:
Curated 21-Jun-2006 by Keseler I , SRI International
Last-Curated ? 24-Mar-2008 by Fulcher C , 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 I , pyrimidine deoxyribonucleotides dephosphorylation , pyrimidine deoxyribonucleotides de novo biosynthesis II

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


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 ]

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;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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

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

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."

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

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

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.

UniProtGOA11: 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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, BIOCYC14A.