Literature summary for 4.2.99.B1 extracted from

Prasad, R.; Beard, W.A.; Strauss, P.R.; Wilson, S.H.
Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism (1998), J. Biol. Chem., 273, 15263-15270.

Search for more literature for 4.2.99.B1

Protein Variants

Protein Variants	Comment	Organism
K72A	2 mM pyridoxal 5'-phosphate, the mutant K72A of the 8-kDa domain and the full-lenghth protein beta-pol exhibit 90 and 80% loss of activity, respectively	Homo sapiens

Inhibitors

Inhibitors	Comment	Organism	Structure
EDTA	5 or 10 mM, inhibits beta-pol dRP lyase activity, in contrast to the 8-kDa domain dRP lyase activity that is slightly stimulated. Higher concentrations, 20 and 40 mM restore the beta-pol activity to a level similar to that in the absence of EDTA. The inhibitory effect of EDTA on the beta-pol ectivity is reversed by 25-100 mM NaCl. The same concentration has no effect on the activity of the 8-kDa domain	Homo sapiens
pyridoxal 5'-phosphate	2 mM, results in 95 and 75% inhibition of the dRP lyase activity of beta-pol and the 8-kDa domain, respectively. The mutant K72A of the 8-kDa domain and the full-length protein beta-pol exhibit 90 and 80% loss of activity, respectively	Homo sapiens

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	intact apurinic/apyrimidinic site	similar to that of preincised apurinic/apyrimidinic site	Homo sapiens
0.0005	-	DNA with a 5'-incised apurinic/apyrimidinic site at position 21	dRP lyase activity of beta-pol. To quantify the kinetic parameters for the release of deoxyribose phosphate from a preincused apurinic/apyrimidinic site-containing DNA, deoxyribose phosphate is examined as a function of apurinic/apyrimidinic site concentration. The catalytic efficiency results in a kcat/Km: 0.00015 mM/s. The catalytic efficiency of the 8-kDa amino-terminal domain is 7fold lower than that of the intact 39-kDa beta-pol	Homo sapiens

Metals/Ions

Metals/Ions	Comment	Organism	Structure
additional information	Mg2+ is not required for the enzyme activity	Homo sapiens
NaCl	up to 50 mM no influence on the dRP lyase acticity of beta-pol or 8-kDa domain occurs. Above 200 mM the activity is completely abolished	Homo sapiens

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
39000	-	consists of a 31 kDa C-terminal and a 8 kDa amino-terminal domain	Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
additional information	Homo sapiens	reaction is part of the DNA base excision repair BER	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	-	-	-

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	reaction is part of the DNA base excision repair BER, enzyme releases 5'-terminal deoxyribose phosphate from preincised apurinic/apyrimidinic site DNA by beta-elimination	Homo sapiens	a

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	the activity exhibited by the 8-kDa domain is over 2 orders of magnitude lower on an intact apurinic/apyrimidinic site, as compared with a preincised apurinic/apyrimidinic site of the DNA	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
DNA with a 5'-incised apurinic/apyrimidinic site at position 21	the uracil-DNA glycosylase-reacted DNA substrate is treated with AP endonuclease in the presence of MgCl2 to create a substrate containing a 5'-incised apurinic/apyrimidinic site. The resulting DNA substrate with a deoxyribose phosphate moiety at the 5'-end and a phosphate at the 3'-terminus is incubated with beta-pol or its amino-terminal 8-kDa domain	Homo sapiens	? + 2-deoxy-D-ribose 5-phosphate	beta-pol is proposed to catalyze the release of the 5'-deoxyribose phosphate moiety from the cleaved apurinic/apyrimidinic site via a beta-elimination mechanism, producing 4-hydroxy-2-pentenal-5-phosphate	?
additional information	reaction is part of the DNA base excision repair BER	Homo sapiens	?	-	?

Subunits

Subunits	Comment	Organism
monomer	1 * 39000, consists of a 31 kDa C-terminal and a 8 kDa amino-terminal domain	Homo sapiens

Synonyms

Synonyms	Comment	Organism
8-kDa domain dRP lyase	-	Homo sapiens
beta-pol dRP lyase	-	Homo sapiens
DNA polymerase beta deoxyribose phosphate lyase	DNA polymerase beta exhibiting both apurinic/apyrimidinic lyase and dRP lyase activity	Homo sapiens
dRP lyase	-	Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
additional information	-	intact apurinic/apyrimidinic site	200fold lower compared to preincised apurinic/apyrimidinic site as substrate	Homo sapiens
0.0075	-	DNA with a 5'-incised apurinic/apyrimidinic site at position 21	dRP lyase activity of beta-pol. To quantify the kinetic parameters for the release of deoxyribose phosphate from a preincused apurinic/apyrimidinic site-containing DNA, deoxyribose phosphate is examined as a function of apurinic/apyrimidinic site concentration. The catalytic efficiency results in a kcat/Km: 0.00015 mM/s. The catalytic efficiency of the 8-kDa amino-terminal domain is 7fold lower than that of the intact 39-kDa beta-pol	Homo sapiens

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	9	optimum for beta-pol dRP lyase activity	Homo sapiens
8	9	optimum for the 8-kDa domain dRP lyase activity	Homo sapiens

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Release 2023.1 (January 2023)