Literature summary for 4.2.99.B1 extracted from

Alonso, A.; Terrados, G.; Picher, A.J.; Giraldo, R.; Blanco, L.; Larraga, V.
An intrinsic 5'-deoxyribose-5-phosphate lyase activity in DNA polymerase beta from Leishmania infantum supports a role in DNA repair (2006), DNA repair, 5, 89-101.

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Cloned(Commentary)

Cloned (Comment)	Organism
expresses in Escherichia coli M15 (pREP4). The protein aggregates as inclusion bodies, solubilized in 5 M guanidinium hydrochloride and 20 mM inidazole-HCl, pH 8.0 and purified	Leishmania infantum

Organism

Organism	UniProt	Comment	Textmining
Leishmania infantum	Q9U6N3	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant protein, expressed in Escherichia coli M15 (pREP4). The protein aggregates as inclusion bodies, solubilized in 5 M guanidinium hydrochloride and 20 mM imidazole-HCl, pH 8.0 and purified	Leishmania infantum

Reaction

Reaction	Comment	Organism	Reaction ID
catalysis of the beta-elimination of the 5' deoxyribose-5-phosphate at an abasic site in DNA where a DNA-(apurinic or apyrimidinic site) lyase has already cleaved the C-O-P bond 3' to the apurinic or apyrimidinic site	concerted reaction of dRP lyase and DNA polymerization of Li Polbeta on a uracil-containing DNA participating in single-nucleotide base excision repair (BER), beta-elimination reaction	Leishmania infantum	a

Source Tissue

Source Tissue	Comment	Organism	Textmining
amastigote	strain MCAN/ES/89/IPZ229/1/89, the enzyme activity varies with the life cycle of Leishmania infantum, being maximal in the intracellular amastigote phase	Leishmania infantum	-
promastigote	strain MHOM/FR/80/LEM75, the enzyme activity varies with the life cycle of Leishmania infantum, being maximal in the intracellular amastigote phase	Leishmania infantum	-

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	the enzyme activity varies with the life cycle of Leishmania infantum, being maximal in the intracellular amastigote phase	Leishmania infantum

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
34-bp-oligonucleotide containing uracil at position 16	labelled with 3'-end by terminal deoxynucleotidyltransferase using [alpha-32P]ddATP and annealed to its complementary oligonucleotide, and pretreated with human uracil-DNA glycosylase and AP endonuclease	Leishmania infantum	19-bp-oligonucleotide + 2-deoxy-D-ribose 5-phosphate	-	?
additional information	the dRP removal proceeds through a beta-elimination, verified by addition of sodium borohydride forming a covalent protein-DNA complex by reduction of the Schiff base intermediate	Leishmania infantum	?	-	?

Subunits

Subunits	Comment	Organism
More	the 8-kDa domain of polymerase beta is responsible for single-stranded DNA binding, 5'-phosphate recognition, and dRP lyase activity, formed by the amino acid residues 1-91 of Li Polbeta. The residues Tyr39, Lys60, Lys68, Lys72, Glu75, and Glu84 play a role in the catalysis. Lys72, identified as the nucleophile in Polbeta is responsible for Schiff base forming during beta-elimination of the dRP moiety	Leishmania infantum

Synonyms

Synonyms	Comment	Organism
5'-deoxyribose-5-phosphate lyase	-	Leishmania infantum
dRP lyase	-	Leishmania infantum
Li polbeta	-	Leishmania infantum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Leishmania infantum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Leishmania infantum

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Release 2023.1 (January 2023)