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4.2.99.B1: DNA 5'-deoxyribose phosphate lyase

This is an abbreviated version!
For detailed information about DNA 5'-deoxyribose phosphate lyase, go to the full flat file.

Word Map on EC 4.2.99.B1

Reaction

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 =

Synonyms

5' dRP lyase, 5'-deoxyribose phosphate lyase, 5'-deoxyribose-5-phosphate lyase, 5'-deoxyribosephosphate lyase, 5'-dRP lyase, 5'-RP lyase, 8-kDa domain dRP lyase, AtPolIA, AtPolIB, beta-pol, beta-pol dRP lyase, deoxyribo-5'-phosphate lyase, DNA beta-polymerase, DNA polymerase beta, DNA polymerase beta deoxyribose phosphate lyase, DNA polymerase gamma, DNA polymerase lambda, DNA polymerase theta, dRP lyase, dRPase, HSV-1 Pol, HSV-1-DNA polymerase, Ku70, Li polbeta, mammalian endonuclease VIII-like protein, NEIL1, NEIL2, pol beta, Pol gamma, pol iota, Pol lambda, Pol theta, PolB, polymerase iota, Rev1, TcPolbeta, TcPolbetaPAK, Trf4, UL30

ECTree

     4 Lyases
         4.2 Carbon-oxygen lyases
             4.2.99 Other carbon-oxygen lyases
                4.2.99.B1 DNA 5'-deoxyribose phosphate lyase

Engineering

Engineering on EC 4.2.99.B1 - DNA 5'-deoxyribose phosphate lyase

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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K72A
-
PCR-based site-directed mutagenesis, deficient in forming a Schiff base intermediate and accumulating an enzyme dRP intermediate without releasing free dRP
D829N/E830Q
-
the polymerase inactive mutant D829N/E830Q retains full 5'-dRP lyase activity. Domain mapping of the 98-kDa enzyme reveals that the 5'-dRP lyase active site resides in a 24-kDa-domain
E71Q
retains wild-type enzyme activity
E75A
about 75% of wild-type enzyme activity
F25W
about 85% of wild-type enzyme activity
H34G
about 45% of wild-type enzyme activity
K310A
eliminates more than 90% of the wild-type dRP lyase activity, indicating that Lys 310 is the main nucleophile involved in the reaction, forming the Schiff base internediate during beta-elimination
K35A/K68A
part of the active site, similar to wild-type enzyme activity
K35A/K68A/K72A
K35A/K72A
part of the active site, above 95% loss of enzyme activity
K35R
part of the active site, no effect on enzyme activity
K35R/K68R/K72R
part of the active site, above 95% loss of enzyme activity
K60A
about 40% of wild-type enzyme activity
K68A/E71Q
retains wild-type enzyme activity
K68A/K72A
about 10% of wild-type enzyme activity
K68R
part of the active site, significant reduction of enzyme activity
K72R
part of the active site, above 95% loss of enzyme activity
K84A
retains wild-type enzyme activity
Y39F
part of the active site, similar to wild-type enzyme activity
D256A
-
site-directed mutagenesis, C-terminal polymerase domain, completely eliminates dRP lyase activity, proficient in DNA synthesis by the polymerase reaction
K35A/K68A/K72A
-
site-directed mutagenesis, amino-terminal dRP lyase domain, completely eliminates dRP lyase activity, proficient in DNA synthesis by the polymerase reaction
K35A/K68A/K72A/D256A
-
site-directed mutagenesis, amino-terminal dRP lyase domain, deficient in dRP lyase and polymerase activity
R283A
-
site-directed mutagenesis, C-terminal polymerase domain, deficient in base excision repair DNA synthesis activity of the polymerase, but has full dRP lyase activity
K552A
site-directed mutagenesis matching the active site of polbeta. The mutant Trf4K552A is overexpressed in a trf4DELTA mutant. The overproduction of Trf4 wild-type increases methylmethane sulfonate resistance similar to that of of the wild-type. The Trf4K552A mutant exhibits hypersensitivity to methylmethane sulfonate, causing double-stranded DNA breaks
additional information