Literature summary for 4.2.99.B1 extracted from

Trasvina-Arenas, C.H.; Baruch-Torres, N.; Cordoba-Andrade, F.J.; Ayala-Garcia, V.M.; Garcia-Medel, P.L.; Diaz-Quezada, C.; Peralta-Castro, A.; Ordaz-Ortiz, J.J.; Brieba, L.G.
Identification of a unique insertion in plant organellar DNA polymerases responsible for 5'-dRP lyase and strand-displacement activities implications for base excision repair (2018), DNA Repair, 65, 1-10 .

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Protein Variants

Protein Variants	Comment	Organism
additional information	construction of several AtPolIB and deletion mutants, AtPolIB exo-DELTAins1, AtPolIB exo-DELTAins2, and AtPolIB exo-DELTAins3, AtPolIB exo- and polymerase mutants harboring deletions in insertion 1, 2 or 3, the mutants, especially AtPolIB exo-DELTAins1 and 3 insertion mutants, shows reduced activity compared to wild-type. Deletions in AtPolIB decrease strand-displacement activities	Arabidopsis thaliana

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	required	Arabidopsis thaliana

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
additional information	Arabidopsis thaliana	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. According to the lyase catalytic mechanism, the epsilon-amino group of a catalytic lysine reacts with C1'-carbon of an AP site producing a Schiff base intermediate	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Arabidopsis thaliana	F4I6M1	-	-
Arabidopsis thaliana	Q84ND9	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
additional information	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. According to the lyase catalytic mechanism, the epsilon-amino group of a catalytic lysine reacts with C1'-carbon of an AP site producing a Schiff base intermediate	Arabidopsis thaliana	?	-	?
additional information	5'-deoxyribose phosphate (5'-dRP)-processed DNA substrate, the processed dsDNA substrate consists of one nucleotide gap and a 5'-dRP group, synthesis overview. 5'-RP lyase activity is dependent on unique plant organellar DNAP insertions	Arabidopsis thaliana	?	-	?

Synonyms

Synonyms	Comment	Organism
5'-RP lyase	-	Arabidopsis thaliana
AtPolIA	-	Arabidopsis thaliana
AtPolIB	-	Arabidopsis thaliana

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Arabidopsis thaliana

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Arabidopsis thaliana

General Information

General Information	Comment	Organism
evolution	AtPolIs are functionally equipped to play a role in short-patch BER suggesting a major role of AtPolIB in a predicted long-patch BER sub-pathway. The acquisition of insertion 1 in the polymerization domain of AtPolIs is a key component in their evolution as BER associated and replicative DNAPs	Arabidopsis thaliana
additional information	residue AtPollB-Lys593 acts as nucleophile for lyase activity and is responsible for 5'-RP lyase activity in AtPolIB. 5'-RP lyase activity is mapped to a single amino acid in insertion 1	Arabidopsis thaliana
physiological function	plant organelles repair damaged DNA using the multi-enzyme base excision repair (BER) pathway. The initial enzymatic steps in BER produce a 5'-deoxyribose phosphate (5'-dRP) moiety that must be removed to allow DNA ligation. DNA polymerases (DNAPs) remove the 5'-dRP moiety using their intrinsic lyase and/or strand-displacement activities during short or long-patch BER sub-pathways, respectively. Arabidopsis thaliana encodes two family-A DNAPs paralogues, AtPolIA and AtPolIB, which are the sole DNAPs in plant organelles identified to date. Both AtPolIs present 5'-dRP lyase activities. AtPolIB performs efficient strand-displacement on a BER-associated 1-nt gap DNA substrate, whereas AtPolIA exhibits only moderate strand-displacement activity. Both lyase and strand-displacement activities are dependent on an amino acid insertion that is exclusively present in plant organellar DNAPs. AtPolIs contribute to long-patch BER by strand-displacement synthesis, but AtPolIs catalyze long and short-patch BER	Arabidopsis thaliana

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Release 2023.1 (January 2023)