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

MetaCyc Enzyme: phosphopentomutase

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

Synonyms: tlr, drm, thyR

Species: Escherichia coli K-12 substr. MG1655

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.

Locations: cytosol

Map Position: [4,617,626 -> 4,618,849]

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

Gene-Reaction Schematic: ?

Instance reaction of [α-D-ribose-1-phosphate ↔ D-ribose 5-phosphate] (5.4.2.7):
i1: α-D-ribose-1-phosphate = α-D-ribose 5-phosphate (5.4.2.-)

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , 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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

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 , purine ribonucleosides degradation

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups [Comment 1]: 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
[UniProt10a]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Acetylation-Modification 287
[Zhang09, UniProt11]
UniProt: N6-acetyllysine.
Metal-Binding-Site 311
[UniProt10a]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 347
[UniProt10a]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 348
[UniProt10a]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 359
[UniProt10a]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;

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

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

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

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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

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

Zhang09: 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Dec 17, 2014, biocyc13.