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Escherichia coli K-12 substr. MG1655 Enzyme: phosphopentomutase



Gene: deoB Accession Numbers: EG10220 (EcoCyc), b4383, ECK4375

Synonyms: tlr, drm, thyR

Regulation Summary Diagram: ?

Summary:
DeoB is a phosphopentomutase which is part of the pathway that utilizes pyrimidine deoxyribonucleoside as a carbon and energy source. Phosphopentomutase is a catabolic enzyme which catalyzes the reversible transfer of a phosphate group between the C1 and the C5 carbon atoms of ribose and deoxyribose, respectively [Leer75].

Mutations in deoB suppresses thymine requirement for growth in thymidylate synthase (thyA) mutants. The deoB mutants were found to be negative for phoshodeoxyribomutase. [MunchPetersen68]

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].

The E. coli phosphopentomutase appears to be biochemically and structurally distinct from mammalian phosphopentomutase [HammerJespersen70, Maliekal07], making them potential targets for antibiotic development.

Gene Citations: [ValentinHansen84, Albrechtsen80, Svenningsen75]

Locations: cytosol

Map Position: [4,617,626 -> 4,618,849] (99.52 centisomes)
Length: 1224 bp / 407 aa

Molecular Weight of Polypeptide: 44.37 kD (from nucleotide sequence), 45.0 kD (experimental) [Leer75 ]

pI: 4.63

Unification Links: ASAP:ABE-0014377 , CGSC:867 , DIP:DIP-48057N , EchoBASE:EB0216 , EcoGene:EG10220 , EcoliWiki:b4383 , ModBase:P0A6K6 , OU-Microarray:b4383 , PortEco:deoB , PR:PRO_000022428 , Pride:P0A6K6 , Protein Model Portal:P0A6K6 , RefSeq:NP_418800 , RegulonDB:EG10220 , SMR:P0A6K6 , String:511145.b4383 , UniProt:P0A6K6

Relationship Links: InterPro:IN-FAMILY:IPR006124 , InterPro:IN-FAMILY:IPR010045 , InterPro:IN-FAMILY:IPR017849 , InterPro:IN-FAMILY:IPR017850 , InterPro:IN-FAMILY:IPR024052 , Pfam:IN-FAMILY:PF01676

In Paralogous Gene Group: 521 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0006015 - 5-phosphoribose 1-diphosphate biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0009117 - nucleotide metabolic process Inferred by computational analysis [GOA01a]
GO:0009264 - deoxyribonucleotide catabolic process Inferred by computational analysis [GOA06]
GO:0043094 - cellular metabolic compound salvage Inferred by computational analysis [GOA01a]
Molecular Function: GO:0008973 - phosphopentomutase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, HammerJespersen70]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0030145 - manganese ion binding Inferred by computational analysis [GOA06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for deoB 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 ? 10-May-2013 by Kubo A , SRI International


Enzymatic reaction of: deoxyribose 1,5-phosphomutase (phosphopentomutase)

Synonyms: phosphodeoxyribomutase, deoxyribomutase, phosphopentomutase

EC Number: 5.4.2.7

2-deoxy-α-D-ribose 1-phosphate <=> 2-deoxy-D-ribose 5-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.

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

Summary:
Inhibition by phosphate is pH dependent. [HammerJespersen70]

Cofactors or Prosthetic Groups: Mn2+ [HammerJespersen70]

Activators (Unknown Mechanism): α-D-ribose 1,5-bisphosphate [HammerJespersen70] , β-glucose 1,6-bisphosphate [HammerJespersen70]

Inhibitors (Unknown Mechanism): Cu2+ [HammerJespersen70] , Cd2+ [HammerJespersen70] , Zn2+ [HammerJespersen70] , Ca2+ [HammerJespersen70] , Fe2+ [HammerJespersen70] , sulfate [HammerJespersen70] , phosphate [HammerJespersen70] , Fe3+ [HammerJespersen70]

Kinetic Parameters:

Substrate
Km (μM)
Citations
2-deoxy-α-D-ribose 1-phosphate
13.0
[HammerJespersen70]

pH(opt): 8 [HammerJespersen70]


Enzymatic reaction of: α-D-ribose 1,5-phosphomutase (phosphopentomutase)

Synonyms: D-ribose 1,5-phosphomutase

EC Number: 5.4.2.7

α-D-ribose-1-phosphate <=> D-ribose 5-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.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , PRPP biosynthesis II , pyrimidine ribonucleosides degradation , purine ribonucleosides degradation

Cofactors or Prosthetic Groups [Comment 5]: Mn2+ [HammerJespersen70]

Kinetic Parameters:

Substrate
Km (μM)
Citations
α-D-ribose-1-phosphate
43.0
[HammerJespersen70]

pH(opt): 8 [HammerJespersen70]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Leer75]
 
Metal-Binding-Site 10
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Acetylation-Modification 287
[Zhang09a, UniProt11a]
UniProt: N6-acetyllysine.
Metal-Binding-Site 311
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 347
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 348
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 359
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b4383 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10220; 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

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

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."

HammerJespersen70: Hammer-Jespersen K, Munch-Petersen A (1970). "Phosphodeoxyribomutase from Escherichia coli. Purification and some properties." Eur J Biochem 1970;17(3);397-407. PMID: 4992818

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

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

Leer75: Leer JC, Hammer-Jespersen K (1975). "Multiple forms of phosphodeoxyribomutase from Escherichia coli. Physical and chemical characterization." Biochemistry 1975;14(3);599-607. PMID: 1089430

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

Maliekal07: Maliekal P, Sokolova T, Vertommen D, Veiga-da-Cunha M, Van Schaftingen E (2007). "Molecular identification of mammalian phosphopentomutase and glucose-1,6-bisphosphate synthase, two members of the alpha-D-phosphohexomutase family." J Biol Chem 282(44);31844-51. PMID: 17804405

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: 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

ValentinHansen84: Valentin-Hansen P, Hammer K, Love Larsen JE, Svendsen I (1984). "The internal regulated promoter of the deo operon of Escherichia coli K-12." Nucleic Acids Res 1984;12(13);5211-24. PMID: 6087276

Zhang07: Zhang N, Chen R, Young N, Wishart D, Winter P, Weiner JH, Li L (2007). "Comparison of SDS- and methanol-assisted protein solubilization and digestion methods for Escherichia coli membrane proteome analysis by 2-D LC-MS/MS." Proteomics 7(4);484-93. PMID: 17309111

Zhang09a: 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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