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: deoxyribose-phosphate aldolase



Gene: deoC Accession Numbers: EG10221 (EcoCyc), b4381, ECK4373

Synonyms: tlr, dra, thyR

Regulation Summary Diagram: ?

Summary:
DeoC is a deoxyribose-phosphate aldolase which is part of the pathway that utilizes pyrimidine deoxyribonucleoside as a carbon and energy source. Deoxyribose-phosphate aldolase catalyzes the aldol reaction between the acetaldehyde donor and glyceraldehyde 3-phosphate acceptor to generate deoxyribose 5-phosphate. It belongs to the class I aldolases which form Schiff base intermediates. [ValentinHansen82]

The purified enzyme may exist as both a monomer and a dimer. The enzyme exists as a monomer in Tris/HCl containing EDTA and as a dimer in phosphate buffer. [ValentinHansen82]

The crystal structure of a covalent complex of deoxyribose phosphate aldolase with deoxyribose 5-phosphate was resolved to 1.05 Å. Site directed mutagenesis of the Schiff base Lys167 and Lys201 were found to be critical to catalysis. [Heine01]

Mutations in deoC suppressed thymine requirement for growth in thymidylate synthase (thyA) mutants. The growth of deoC mutants were inhibited by deoxyribonucleosides, thymidine, or deoxyadenosines. The mutants were sensitive to deoxyribonucleosides as a result of deoxyribose 5-phosphate accumulation. [MunchPetersen68, MunchPetersen70].

The deo designation is used to indicate a gene determining an enzyme necessary for growth on deoxythymidine or deoxyuridine as the sole carbon source. [Dale67]

The deo operon consists of four enzymes: deoxyriboaldolase, thymidine phosphorylase, phosphodeoxyribomutase and purine nucleoside phosphorylase [Ahmad69]. This operon has an unusual and complex pattern of regulation [HammerJespersen75, ValentinHansen79] including two regulatory proteins encoded by the genes cytR and deoR [MunchPetersen72].

Gene Citations: [Albrechtsen80, Svenningsen75]

Locations: cytosol, membrane

Map Position: [4,615,346 -> 4,616,125] (99.48 centisomes)
Length: 780 bp / 259 aa

Molecular Weight of Polypeptide: 27.734 kD (from nucleotide sequence), 27.2 kD (experimental) [ValentinHansen82 ]

pI: 5.78

Unification Links: ASAP:ABE-0014371 , CGSC:866 , EchoBASE:EB0217 , EcoGene:EG10221 , EcoliWiki:b4381 , ModBase:P0A6L0 , OU-Microarray:b4381 , PortEco:deoC , PR:PRO_000022429 , Pride:P0A6L0 , Protein Model Portal:P0A6L0 , RefSeq:NP_418798 , RegulonDB:EG10221 , SMR:P0A6L0 , String:511145.b4381 , UniProt:P0A6L0

Relationship Links: InterPro:IN-FAMILY:IPR002915 , InterPro:IN-FAMILY:IPR011343 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR023649 , Panther:IN-FAMILY:PTHR10889 , PDB:Structure:1JCJ , PDB:Structure:1JCL , PDB:Structure:1KTN , PDB:Structure:1P1X , Pfam:IN-FAMILY:PF01791

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009264 - deoxyribonucleotide catabolic process Inferred from experiment Inferred by computational analysis [GOA01a, Dale67]
GO:0015949 - nucleobase-containing small molecule interconversion Inferred from experiment [Dale67]
GO:0016052 - carbohydrate catabolic process Inferred from experiment Inferred by computational analysis [GOA06, ValentinHansen82]
GO:0046386 - deoxyribose phosphate catabolic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0004139 - deoxyribose-phosphate aldolase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Heine01, ValentinHansen82]
GO:0016829 - lyase activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, ValentinHansen82]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for deoC 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 ? 14-May-2013 by Kubo A , SRI International


Enzymatic reaction of: deoxyribose-phosphate aldolase

Synonyms: phosphodeoxyriboaldolase, deoxyriboaldolase, DR aldolase, 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase, 2-deoxy-D-ribose-5-phophate acetaldehyde lyase

EC Number: 4.1.2.4

2-deoxy-D-ribose 5-phosphate <=> acetaldehyde + D-glyceraldehyde 3-phosphate

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. [Racker52]

Alternative Substrates for D-glyceraldehyde 3-phosphate: dihydroxyacetone phosphate [Comment 5 , Racker52 ]

In Pathways: superpathway of purine deoxyribonucleosides degradation , superpathway of pyrimidine deoxyribonucleosides degradation , 2'-deoxy-α-D-ribose 1-phosphate degradation

Inhibitors (Unknown Mechanism): chloral hydrate [Racker52] , octan-1-ol [Racker52] , propanal [Racker52]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
2-deoxy-D-ribose 5-phosphate
640.0
[Heine01, BRENDA14]
2-deoxy-D-ribose 5-phosphate
640.0
68.0
[DeSantis03, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[ValentinHansen82]
 
Sequence-Conflict 18
[ValentinHansen82, UniProt10a]
Alternate sequence: T → N; UniProt: (in Ref. 1; CAA26974);
Acetylation-Modification 167
[Zhang09c, UniProt11]
UniProt: N6-acetyllysine.
Active-Site 167
[Heine01, UniProt11]
UniProt: Schiff-base intermediate with acetaldehyde.
Active-Site 201
[Heine01, UniProt11]
.


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4381 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10221; confirmed by SwissProt match.


References

Ahmad69: Ahmad SI, Pritchard RH (1969). "A map of four genes specifying enzymes involved in catabolism of nucleosides and deoxynucleosides in Escherichia coli." Mol Gen Genet 104(4);351-9. PMID: 4904508

Albrechtsen80: Albrechtsen H, Ahmad SI (1980). "Regulation of the synthesis of nucleoside catabolic enzymes in Escherichia coli: further analysis of a deo Oc mutant strain." Mol Gen Genet 1980;179(2);457-60. PMID: 6780756

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Dale67: Dale B, Greenberg GR (1967). "Genetic mapping of a mutation in Escherichia coli showing reduced activity of thymidine phosphorylase." J Bacteriol 94(3);778-9. PMID: 5340684

DeSantis03: DeSantis G, Liu J, Clark DP, Heine A, Wilson IA, Wong CH (2003). "Structure-based mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase." Bioorg Med Chem 11(1);43-52. PMID: 12467706

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

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."

HammerJespersen75: Hammer-Jespersen K, Munch-Ptersen A (1975). "Multiple regulation of nucleoside catabolizing enzymes: regulation of the deo operon by the cytR and deoR gene products." Mol Gen Genet 137(4);327-35. PMID: 171553

Heine01: Heine A, DeSantis G, Luz JG, Mitchell M, Wong CH, Wilson IA (2001). "Observation of covalent intermediates in an enzyme mechanism at atomic resolution." Science 294(5541);369-74. PMID: 11598300

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

MunchPetersen68: Munch-Petersen A (1968). "Thymineless mutants of Escherichia coli with deficiencies in deoxyribomutase and deoxyriboaldolase." Biochim Biophys Acta 161(1);279-82. PMID: 4873559

MunchPetersen70: Munch-Petersen A (1970). "Deoxyribonucleoside catabolism and thymine incorporation in mutants of Escherichia coli lacking deoxyriboaldolase." Eur J Biochem 15(1);191-202. PMID: 4923156

MunchPetersen72: Munch-Petersen A, Nygaard P, Hammer-Jespersen K, Fiil N (1972). "Mutants constitutive for nucleoside-catabolizing enzymes in Escherichia coli K12. Isolation, charactrization and mapping." Eur J Biochem 27(2);208-15. PMID: 4559263

Racker52: Racker E (1952). "Enzymatic synthesis and breakdown of desoxyribose phosphate." J Biol Chem 196(1);347-65. PMID: 12980976

Racker52a: Racker E "Enzymatic synthesis and breakdown of deoxyribose phosphate." J Biol Chem 1952;196:347-365.

Svenningsen75: Svenningsen BA (1975). "Regulated in vitro synthesis of the enzymes of the deo operon of Escerichia coli. properties of the DNA directed system." Mol Gen Genet 1975;137(4);289-304. PMID: 810659

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

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

ValentinHansen79: Valentin-Hansen P, Hammer-Jespersen K, Buxton RS (1979). "Evidence for the existence of three promoters for the deo operon of Escherichia coli K12 in vitro." J Mol Biol 133(1);1-17. PMID: 231107

ValentinHansen82: Valentin-Hansen P, Boetius F, Hammer-Jespersen K, Svendsen I (1982). "The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence of the enzyme." Eur J Biochem 1982;125(3);561-6. PMID: 6749498

Zhang09c: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Amouyal89: Amouyal M, Mortensen L, Buc H, Hammer K (1989). "Single and double loop formation when deoR repressor binds to its natural operator sites." Cell 1989;58(3);545-51. PMID: 2667765

Brikun96: Brikun I, Suziedelis K, Stemmann O, Zhong R, Alikhanian L, Linkova E, Mironov A, Berg DE (1996). "Analysis of CRP-CytR interactions at the Escherichia coli udp promoter." J Bacteriol 1996;178(6);1614-22. PMID: 8626289

Chahla03: Chahla M, Wooll J, Laue TM, Nguyen N, Senear DF (2003). "Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon." Biochemistry 42(13);3812-25. PMID: 12667072

Gavigan99: Gavigan SA, Nguyen T, Nguyen N, Senear DF (1999). "Role of multiple CytR binding sites on cooperativity, competition, and induction at the Escherichia coli udp promoter." J Biol Chem 1999;274(23);16010-9. PMID: 10347150

Gerlach91: Gerlach P, Sogaard-Andersen L, Pedersen H, Martinussen J, Valentin-Hansen P, Bremer E (1991). "The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12." J Bacteriol 1991;173(17);5419-30. PMID: 1715855

GonzalezGil96: Gonzalez-Gil G, Bringmann P, Kahmann R (1996). "FIS is a regulator of metabolism in Escherichia coli." Mol Microbiol 22(1);21-9. PMID: 8899705

Holst92: Holst B, Sogaard-Andersen L, Pedersen H, Valentin-Hansen P (1992). "The cAMP-CRP/CytR nucleoprotein complex in Escherichia coli: two pairs of closely linked binding sites for the cAMP-CRP activator complex are involved in combinatorial regulation of the cdd promoter." EMBO J 11(10);3635-43. PMID: 1327747

Holt10: Holt AK, Senear DF (2010). "An unusual pattern of CytR and CRP binding energetics at Escherichia coli cddP suggests a unique blend of class I and class II mediated activation." Biochemistry 49(3);432-42. PMID: 20000490

Jorgensen98: Jorgensen CI, Kallipolitis BH, Valentin-Hansen P (1998). "DNA-binding characteristics of the Escherichia coli CytR regulator: a relaxed spacing requirement between operator half-sites is provided by a flexible, unstructured interdomain linker." Mol Microbiol 27(1);41-50. PMID: 9466254

Larsen87: Larsen JE, Albrechtsen B, Valentin-Hansen P (1987). "Analysis of the terminator region after the deoCABD operon of Escherichia coli K-12 using a new class of single copy number operon-fusion vectors." Nucleic Acids Res 1987;15(13);5125-40. PMID: 3299264

Mayes77: Mayes DG (1977). "A comparison of menstrual bleeding patterns associated with three IUD models: an example of reference period analysis." J Biosoc Sci 9(1);121-35. PMID: 845188

MedinaRivera11: Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J, van Helden J (2011). "Theoretical and empirical quality assessment of transcription factor-binding motifs." Nucleic Acids Res 39(3);808-24. PMID: 20923783

Meibom00: Meibom KL, Kallipolitis BH, Ebright RH, Valentin-Hansen P (2000). "Identification of the subunit of cAMP receptor protein (CRP) that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression." J Biol Chem 275(16);11951-6. PMID: 10766824

Mollegaard93: Mollegaard NE, Rasmussen PB, Valentin-Hansen P, Nielsen PE (1993). "Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deoP2 promoter." J Biol Chem 268(23);17471-7. PMID: 8394345

Pedersen91: Pedersen H, Sogaard-Andersen L, Holst B, Valentin-Hansen P (1991). "Heterologous cooperativity in Escherichia coli. The CytR repressor both contacts DNA and the cAMP receptor protein when binding to the deoP2 promoter." J Biol Chem 266(27);17804-8. PMID: 1655726

Pedersen97: Pedersen H, Valentin-Hansen P (1997). "Protein-induced fit: the CRP activator protein changes sequence-specific DNA recognition by the CytR repressor, a highly flexible LacI member." EMBO J 16(8);2108-18. PMID: 9155036

Perini96: Perini LT, Doherty EA, Werner E, Senear DF (1996). "Multiple specific CytR binding sites at the Escherichia coli deoP2 promoter mediate both cooperative and competitive interactions between CytR and cAMP receptor protein." J Biol Chem 271(52);33242-55. PMID: 8969182

Shin01: Shin M, Kang S, Hyun SJ, Fujita N, Ishihama A, Valentin-Hansen P, Choy HE (2001). "Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor." EMBO J 20(19);5392-9. PMID: 11574471

SogaardAndersen90: Sogaard-Andersen L, Martinussen J, Mollegaard NE, Douthwaite SR, Valentin-Hansen P (1990). "The CytR repressor antagonizes cyclic AMP-cyclic AMP receptor protein activation of the deoCp2 promoter of Escherichia coli K-12." J Bacteriol 1990;172(10);5706-13. PMID: 2170326

SogaardAndersen90a: Sogaard-Andersen L, Mollegaard NE, Douthwaite SR, Valentin-Hansen P (1990). "Tandem DNA-bound cAMP-CRP complexes are required for transcriptional repression of the deoP2 promoter by the CytR repressor in Escherichia coli." Mol Microbiol 4(9);1595-601. PMID: 1962841

Showing only 20 references. To show more, press the button "Show all references".


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, BIOCYC14A.