Disease relevance of deoxyribose-5-phosphate

• Highly purified exonuclease I isolated from an over-producing stain contains high levels of dRpase activity; it catalyzes the release of deoxyribose-5-phosphate from an AP site incised with endonuclease IV of E. coli and the release of 4-hydroxy-2-pentenal-5-phosphate from an AP site incised by the AP lyase activity of endonuclease III of E. coli [1].
• The crystal structure of 2-deoxyribose-5-phosphate aldolase from Thermus thermophilus HB8 has been determined with and without the substrate at atomic resolution [2].
• Deoxyribose-5-phosphate aldolase from Salmonella typhimurium [3].
• Induction of deoxyribose-5-phosphate aldolase of Bacillus cereus by deoxyribonucleosides [4].

High impact information on deoxyribose-5-phosphate

• During short-patch base excision repair, the excision of a 5'-terminal 2-deoxyribose-5-phosphate moiety of the downstream strand by the 5'-2-deoxyribose-5-phosphate lyase activity of either DNA polymerase beta or lambda is believed to occur after each respective enzyme catalyzes gap-filling DNA synthesis [5].
• These results suggest roles for the Ape1 exonuclease during BER after both DNA repair synthesis and excision of the abasic deoxyribose-5-phosphate by polymerase beta [6].
• Tg does not affect 5'-sugar phosphate removal by the 2-deoxyribose-5-phosphate (dRP) lyase activity of DNA polymerase beta, but further processing of the strand break by purified DNA ligase III was slightly diminished [7].
• Both Fpg and S3 also contain a deoxyribophosphodiesterase (dRpase) activity that removes 2-deoxyribose-5-phosphate at an incised 5' apurinic/apyrimidinic (AP) sites via a beta-elimination reaction [8].
• The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution [9].

Biological context of deoxyribose-5-phosphate

• Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution [9].
• The 3' --> 5' exonuclease activity is shown to be highly dependent upon the identity of the nascent 3' base pair and to be inhibited when 2-deoxyribose-5-phosphate, rather than phosphate, constitutes the 5' moiety of the nick [10].
• Incubation of plasmid DNA with reduced RSU-1069 in the presence of either phosphate or deoxyribose-5-phosphate at concentrations greater than 0.35 mol dm-3 prevents strand breakage, whereas 1.2 mol dm-3 deoxyribose does not protect against strand breakage formation [11].

Associations of deoxyribose-5-phosphate with other chemical compounds

• Reaction sequences or loci of particular importance are also described: phosphofructokinases, NADH oxidase, thioredoxin complex, deoxyribose-5-phosphate aldolase, and lactate, malate, and glutamate dehydrogenases [12].

Gene context of deoxyribose-5-phosphate

• Accumulation of deoxyribose-5-phosphate as a possible reason for inhibition is ruled out since the strains are deoB- (formerly drm-) and synthesize deoxyriboaldolase constitutively [13].
• The base excision repair (BER) process requires removal of an abasic deoxyribose-5-phosphate group, a catalytic activity that has been demonstrated for the N-terminal 8 kDa domain of DNA polymerase beta (Pol beta), and for the homologous domain of DNA polymerase lambda (Pol lambda) [14].
• We show that AP sites in DNA are easily removed by the 3'-5' exonuclease activity of the Klenow fragment and that they are excised as deoxyribose-5-phosphate [15].

Analytical, diagnostic and therapeutic context of deoxyribose-5-phosphate

• Crystallization and preliminary crystallographic data for class I deoxyribose-5-phosphate aldolase from Escherichia coli: an application of reverse screening [16].

References