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Escherichia coli K-12 substr. MG1655 Enzyme: cytidylate kinase



Gene: cmk Accession Numbers: EG11265 (EcoCyc), b0910, ECK0901

Synonyms: ycaF, mssA, ycaG

Regulation Summary Diagram: ?

Summary:
Cytidylate kinase (Cmk) rephosphorylates CMP and dCMP that is produced by the turnover of nucleic acids and CDP diglycerides. Cmk is not an essential enzyme, because CMP is not an intermediate in the de novo pathway for the synthesis of CTP. Unlike the eukaryotic UMP/CMP kinases, this enzyme is specific for CMP or dCMP.

Crystal strutures of Cmk have been solved [Bucurenci96, Briozzo98, Bertrand02]. They dynamic properties of the ATP binding site were probed with a fluorescent dATP analog, and molecular modeling suggested that ATP-mediated induced fit is modulated by CMP binding, which leads to a closed conformation of the active site [Li00]. Residues involved in the interaction with the pentose moiety [Bertrand02] and the pyrimidine ring of CMP [Ofiteru07] have been identified in the crystal structure and functionally verified by site-directed mutagenesis.

cmk was isolated as a multicopy suppressor of the cold-sensitive growth phenotype of the smbA2 allele of pyrH, which encodes the UMP kinase [Yamanaka94]. A cmk deletion strain is cold sensitive; its CMP and dCMP pools are elevated 30-fold, and its rate of replication elongation is decreased [Fricke95]. While cmk is not essential for gowth of E. coli, it is required for growth of bacteriophage T7 in E. coli [Qimron06].

MssA: "multicopy suppressor of smbA2 A" [Yamanaka94]

Cmk: "CMP kinase" [Fricke95]

Gene Citations: [Pedersen84]

Locations: cytosol

Map Position: [960,424 -> 961,107] (20.7 centisomes)
Length: 684 bp / 227 aa

Molecular Weight of Polypeptide: 24.746 kD (from nucleotide sequence), 24.6 kD (experimental) [Bucurenci96 ]

Unification Links: ASAP:ABE-0003101 , CGSC:31736 , EchoBASE:EB1244 , EcoGene:EG11265 , EcoliWiki:b0910 , ModBase:P0A6I0 , OU-Microarray:b0910 , PortEco:cmk , PR:PRO_000022301 , Pride:P0A6I0 , Protein Model Portal:P0A6I0 , RefSeq:NP_415430 , RegulonDB:EG11265 , SMR:P0A6I0 , String:511145.b0910 , UniProt:P0A6I0

Relationship Links: InterPro:IN-FAMILY:IPR003136 , InterPro:IN-FAMILY:IPR011994 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR21299:SF2 , PDB:Structure:1CKE , PDB:Structure:1KDO , PDB:Structure:1KDP , PDB:Structure:1KDR , PDB:Structure:1KDT , PDB:Structure:2CMK , PDB:Structure:2FEM , PDB:Structure:2FEO , Pfam:IN-FAMILY:PF02224

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Bucurenci96]
GO:0046939 - nucleotide phosphorylation Inferred by computational analysis Inferred from experiment [Bucurenci96, GOA06, GOA01a]
GO:0006220 - pyrimidine nucleotide metabolic process Inferred by computational analysis [GOA06]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0004127 - cytidylate kinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Bucurenci96]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides pyrimidine ribonucleotide biosynthesis
metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for cmk knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Credits:
Last-Curated ? 15-May-2013 by Keseler I , SRI International


Enzymatic reaction of: CMP kinase (cytidylate kinase)

Synonyms: CK, cytidine monophosphate kinase, CMP kinase, ATP:CMP phosphotransferase, cytidylate kinase

EC Number: 2.7.4.25

ATP + CMP <=> ADP + CDP

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Bucurenci96]

Alternative Substrates for ATP: dATP [Bucurenci96 ] , GTP [Bucurenci96 ]

Alternative Substrates for CMP: UMP [Bucurenci96 ]

In Pathways: superpathway of pyrimidine ribonucleosides salvage , salvage pathways of pyrimidine ribonucleotides , CMP phosphorylation

Summary:
Both ADP and CDP are slightly inhibitory at concentrations above 0.3 mM [Bucurenci96].

Cofactors or Prosthetic Groups: Mg2+

Kinetic Parameters:

Substrate
Km (μM)
Vmax (µmol mg-1 min-1)
Citations
GTP
640.0
233.0
[Bucurenci96]
CDP
52.0
[Bucurenci96]
CMP
35.0
250.0
[Bucurenci96]
dATP
87.0
175.0
[Bucurenci96]
ADP
25.0
[Bucurenci96]
ATP
38.0
189.0
[Bucurenci96]
UMP
930.0
2.0
[Bucurenci96]


Enzymatic reaction of: dCMP kinase (cytidylate kinase)

Synonyms: deoxycytidylate kinase

EC Number: 2.7.4.25

ATP + dCMP <=> ADP + dCDP

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 dCMP: dUMP [Bucurenci96 ]

In Pathways: pyrimidine deoxyribonucleotide phosphorylation

Kinetic Parameters:

Substrate
Km (μM)
Vmax (µmol mg-1 min-1)
Citations
dCMP
94.0
263.0
[Bucurenci96]
dUMP
1460.0
0.35
[Bucurenci96]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Bucurenci96]
 
Nucleotide-Phosphate-Binding-Region 12 -> 20
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: by similarity;
Sequence-Conflict 164
[Pedersen84, UniProt10]
Alternate sequence: E → V; UniProt: (in Ref. 1; CAA25360);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0910 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11265; 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

Bertrand02: Bertrand T, Briozzo P, Assairi L, Ofiteru A, Bucurenci N, Munier-Lehmann H, Golinelli-Pimpaneau B, Barzu O, Gilles AM (2002). "Sugar specificity of bacterial CMP kinases as revealed by crystal structures and mutagenesis of Escherichia coli enzyme." J Mol Biol 315(5);1099-110. PMID: 11827479

Briozzo98: Briozzo P, Golinelli-Pimpaneau B, Gilles AM, Gaucher JF, Burlacu-Miron S, Sakamoto H, Janin J, Barzu O (1998). "Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity." Structure 6(12);1517-27. PMID: 9862805

Bucurenci96: Bucurenci N, Sakamoto H, Briozzo P, Palibroda N, Serina L, Sarfati RS, Labesse G, Briand G, Danchin A, Bărzu O, Gilles AM (1996). "CMP kinase from Escherichia coli is structurally related to other nucleoside monophosphate kinases." J Biol Chem 271(5);2856-62. PMID: 8576266

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

Fricke95: Fricke J, Neuhard J, Kelln RA, Pedersen S (1995). "The cmk gene encoding cytidine monophosphate kinase is located in the rpsA operon and is required for normal replication rate in Escherichia coli." J Bacteriol 1995;177(3);517-23. PMID: 7836281

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."

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

Li00: Li de La Sierra IM, Gallay J, Vincent M, Bertrand T, Briozzo P, Barzu O, Gilles AM (2000). "Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling." Biochemistry 39(51);15870-8. PMID: 11123913

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

Ofiteru07: Ofiteru A, Bucurenci N, Alexov E, Bertrand T, Briozzo P, Munier-Lehmann H, Gilles AM (2007). "Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase." FEBS J 274(13);3363-73. PMID: 17542990

Pedersen84: Pedersen S, Skouv J, Kajitani M, Ishihama A (1984). "Transcriptional organization of the rpsA operon of Escherichia coli." Mol Gen Genet 196(1);135-40. PMID: 6384724

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

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

UniProt10a: 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 the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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

Yamanaka94: Yamanaka K, Ogura T, Koonin EV, Niki H, Hiraga S (1994). "Multicopy suppressors, mssA and mssB, of an smbA mutation of Escherichia coli." Mol Gen Genet 243(1);9-16. PMID: 8190075

Other References Related to Gene Regulation

Boni01: Boni IV, Artamonova VS, Tzareva NV, Dreyfus M (2001). "Non-canonical mechanism for translational control in bacteria: synthesis of ribosomal protein S1." EMBO J 20(15);4222-32. PMID: 11483525

Christiansen81: Christiansen L, Pedersen S (1981). "Cloning, restriction endonuclease mapping and post-transcriptional regulation of rpsA, the structural gene for ribosomal protein S1." Mol Gen Genet 181(4);548-51. PMID: 6267426

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220

Skouv90: Skouv J, Schnier J, Rasmussen MD, Subramanian AR, Pedersen S (1990). "Ribosomal protein S1 of Escherichia coli is the effector for the regulation of its own synthesis." J Biol Chem 265(28);17044-9. PMID: 2120211


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 Mon Dec 22, 2014, biocyc11.