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
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: uridine kinase / cytidine kinase



Gene: udk Accession Numbers: EG11701 (EcoCyc), b2066, ECK2060

Regulation Summary Diagram: ?

Summary:
Uridine-cytidine kinase phosphorylates both uridine and cytidine; GTP and dGTP are the most efficient phosphate donors [ValentinHansen78].

Uridine-cytidine kinase was found to have a molecular weight of 90,000 by gel filtration and is thus likely not monomeric [ValentinHansen78].

Overexpression of uridine-cytidine kinase inhibits growth of the bacteriophage T7, particularly in a T7 gp0.7 mutant [Qimron06], due to inadequate inhibition of host RNA polymerase [Qimron08]. Overexpression of Udk mimics the absence of Gp2 during T7 infection [Shadrin12].

Citations: [Neuhard93]

Gene Citations: [Neuhard76]

Locations: cytosol

Map Position: [2,140,331 <- 2,140,972] (46.13 centisomes)
Length: 642 bp / 213 aa

Molecular Weight of Polypeptide: 24.353 kD (from nucleotide sequence)

pI: 6.81

Unification Links: ASAP:ABE-0006840 , CGSC:42 , DIP:DIP-36012N , EchoBASE:EB1652 , EcoGene:EG11701 , EcoliWiki:b2066 , ModBase:P0A8F4 , OU-Microarray:b2066 , PortEco:udk , PR:PRO_000024162 , Pride:P0A8F4 , Protein Model Portal:P0A8F4 , RefSeq:NP_416570 , RegulonDB:EG11701 , SMR:P0A8F4 , String:511145.b2066 , UniProt:P0A8F4

Relationship Links: InterPro:IN-FAMILY:IPR000764 , InterPro:IN-FAMILY:IPR006083 , InterPro:IN-FAMILY:IPR026008 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR10285:SF6 , Pfam:IN-FAMILY:PF00485 , Prints:IN-FAMILY:PR00988

In Paralogous Gene Group: 372 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009224 - CMP biosynthetic process Inferred from experiment [ValentinHansen78]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0008655 - pyrimidine-containing compound salvage Inferred by computational analysis [GOA06]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11]
GO:0044206 - UMP salvage Inferred by computational analysis [UniProtGOA12]
GO:0044211 - CTP salvage Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004849 - uridine kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, ValentinHansen78, Neuhard76]
GO:0043771 - cytidine kinase activity Inferred from experiment [ValentinHansen78]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0016773 - phosphotransferase activity, alcohol group as acceptor Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for udk 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:
Last-Curated ? 03-Jan-2013 by Keseler I , SRI International


Enzymatic reaction of: uridine kinase

EC Number: 2.7.1.48

uridine + ATP <=> UMP + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of pyrimidine ribonucleosides salvage , pyrimidine ribonucleosides salvage I

Credits:
Imported from MetaCyc 24-Jan-2013 by Caspi R , SRI International

Summary:
Activity with ATP is about 10% of that with GTP [Sehgal77].


Enzymatic reaction of: cytidine kinase

EC Number: 2.7.1.48

cytidine + ATP <=> CMP + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of pyrimidine ribonucleosides salvage , pyrimidine ribonucleosides salvage I

Credits:
Imported from MetaCyc 24-Jan-2013 by Caspi R , SRI International

Summary:
Activity with ATP is about 10% of that with GTP [Sehgal77].


Enzymatic reaction of: uridine kinase

Synonyms: uridine monophosphokinase, pyrimidine ribonucleoside kinase, ATP:uridine 5'-phosphotransferase

EC Number: 2.7.1.48

uridine + GTP <=> UMP + GDP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for GTP: ATP

In Pathways: salvage pathways of pyrimidine ribonucleotides

Inhibitors (Competitive): 5'-iodo-5'-deoxyuridine [ValentinHansen78] , 5'-amino-5'-deoxyuridine [ValentinHansen78] , 5'-azido-5-deoxyuridine [ValentinHansen78] , 5'-deoxyuridine [ValentinHansen78]

Inhibitors (Unknown Mechanism): CTP [ValentinHansen78] , UTP [ValentinHansen78]

Kinetic Parameters:

Substrate
Km (μM)
Citations
uridine
350.0
[ValentinHansen78]

pH(opt): 7.8 [ValentinHansen78]


Enzymatic reaction of: cytidine kinase

Synonyms: pyrimidine ribonucleoside kinase

EC Number: 2.7.1.48

cytidine + GTP <=> CMP + GDP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

Alternative Substrates for GTP: ATP

In Pathways: salvage pathways of pyrimidine ribonucleotides

Inhibitors (Competitive): 5'-iodo-5'-deoxyuridine [ValentinHansen78] , 5'-amino-5'-deoxyuridine [ValentinHansen78] , 5'-azido-5-deoxyuridine [ValentinHansen78] , 5'-deoxyuridine [ValentinHansen78]

Inhibitors (Unknown Mechanism): CTP [ValentinHansen78] , UTP [ValentinHansen78]

Kinetic Parameters:

Substrate
Km (μM)
Citations
cytidine
130.0
[ValentinHansen78]

pH(opt): 7.8 [ValentinHansen78]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 15 -> 22
[UniProt10]
UniProt: ATP; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2066 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11701; confirmed by SwissProt match.


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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

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

Neuhard76: Neuhard J, Thomassen E (1976). "Altered deoxyribonucleotide pools in P2 eductants of Escherichia coli K-12 due to deletion of the dcd gene." J Bacteriol 1976;126(2);999-1001. PMID: 177407

Neuhard93: Neuhard J, Tarpo L (1993). "Location of the udk gene on the physical map of Escherichia coli." J Bacteriol 175(17);5742-3. PMID: 8366067

Qimron06: Qimron U, Marintcheva B, Tabor S, Richardson CC (2006). "Genomewide screens for Escherichia coli genes affecting growth of T7 bacteriophage." Proc Natl Acad Sci U S A 103(50);19039-44. PMID: 17135349

Qimron08: Qimron U, Kulczyk AW, Hamdan SM, Tabor S, Richardson CC (2008). "Inadequate inhibition of host RNA polymerase restricts T7 bacteriophage growth on hosts overexpressing udk." Mol Microbiol 67(2);448-57. PMID: 18067538

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sehgal77: Sehgal A, Hoffmann JC (1977). "Serum LH levels in intact & ovariectomized female rats during puberty." Indian J Exp Biol 15(3);229-31. PMID: 21137

Shadrin12: Shadrin A, Sheppard C, Savalia D, Severinov K, Wigneshweraraj S (2012). "Overexpression of Escherichia coli udk mimics the absence of T7 Gp2 function and thereby abrogates successful infection by T7 phage." Microbiology. PMID: 23242801

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

ValentinHansen78: Valentin-Hansen P (1978). "Uridine-cytidine kinase from Escherichia coli." Methods Enzymol 1978;51;308-14. PMID: 211379

Other References Related to Gene Regulation

Shimada13a: Shimada T, Kori A, Ishihama A (2013). "Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli." FEMS Microbiol Lett 344(2);159-65. PMID: 23651393


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 Thu Nov 27, 2014, BIOCYC14B.