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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: ?

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 [GOA01]
GO:0009117 - nucleotide metabolic process Inferred by computational analysis [GOA01]
GO:0009264 - deoxyribonucleotide catabolic process Inferred by computational analysis [GOA06]
GO:0043094 - cellular metabolic compound salvage Inferred by computational analysis [GOA01]
Molecular Function: GO:0008973 - phosphopentomutase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, HammerJespersen70]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA01]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0030145 - manganese ion binding Inferred by computational analysis [GOA06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

MultiFun Terms: metabolism central intermediary metabolism nucleotide and nucleoside conversions

Credits:
Imported from EcoCyc 27-Jan-2015 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 27-Jan-2015 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 27-Jan-2015 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
[UniProt10]
UniProt: Manganese; Non-Experimental Qualifier: by similarity;
Acetylation-Modification 287
[Zhang09, UniProt11]
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;

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, 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."

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

UniProt10: 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 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."

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 19.0 on Sun Apr 26, 2015, biocyc12.