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
-
4.2.99.B1
-
glycosylases
-
polymerases
-
abasic
-
neils
-
ape1
-
8-oxoguanine
-
gap-filling
-
nei-like
-
translesion
-
8-oxog
-
base-specific
-
5-hydroxyuracil
-
long-patch
-
spiroiminodihydantoin
-
y-family
- 4.2.99.B1
- glycosylases
- polymerases
-
abasic
-
neils
- ape1
- 8-oxoguanine
-
gap-filling
-
nei-like
-
translesion
-
8-oxog
-
base-specific
- 5-hydroxyuracil
-
long-patch
- spiroiminodihydantoin
-
y-family
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
4.2.99.B1 DNA 5'-deoxyribose phosphate lyaseAdvanced search results
results (
results (Substrates Products
Substrates Products on EC 4.2.99.B1 - DNA 5'-deoxyribose phosphate lyase
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
top
SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
25-mer-deoxyoligonucleotide 3'-labeled uracil-containing DNA duplex
? + 2-deoxy-D-ribose 5-phosphate
-
[32P]-labeled substarte, treated with uracil-DNA glycosylase and apurinic/apyrimidinic endonuclease
the products are stabilized by NaBH4 reduction of the Schiff base, formed between the catalytic nucleophile of the dRP lyase and C1' of rhe 2-deoxyribose 5-phosphate site, verifying the dRP removal by a beta-elimination
-
?
28-mer deoxyoligonucleotide with a 5' uracil residue
?
-
pretreated with Eschericia coli uracil N-glycosylase
-
-
?
34-bp oligonucleotide containing uracil at position 16
? + 2-deoxy-D-ribose 5-phosphate
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
-
-
?
34-bp-deoxyoligonucleotide duplex containing a uracil residue at position 16
? + 2-deoxy-D-ribose phosphate
-
preincised [32P] apurinic/apyrimidinic site containing DNA, pretreated with uracil DNA-glycosylase and AP endonuclease
the reaction products are separarted by electrophoresis
-
?
34-bp-oligonucleotide containing uracil at position 16
19-bp-oligonucleotide + 2-deoxy-D-ribose 5-phosphate
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
-
-
?
34-mer-deoxyoligonucleotide containing a uracil residue at position 16
18-mer-deoxyoligonucleotide + 2-deoxy-D-ribose 5-phosphate
-
pretreated with uracil-N-glycosylase and apurunic/apyrimidinic endonuclease
-
-
?
35-bp-deoxyoligonucleotide duplex containing a uracil residue at position 15
? + 2-deoxy-D-ribose phosphate
-
in vitro single-nucleotide base excision DNA repair assay, containing amongst others uracil DNA-glycosylase, AP endonuclease and ligase I
-
-
?
49-bp oligodeoxynucleotide containing uracil at position 21
? + 2-deoxy-D-ribose 5-phosphate
-
labelled at 3'-end with [alpha-32P]ddATP by terminal deoxynucleotidyl transferase and annealed to an unlabelled complementary strand containing a G residue opposite the uracil. Before use, the substrate is treated with uracil-DNA glycosylase and AP endonuclease to generate a single nucleotide gap directly upstream from the labelled fragment containing a deoxyribose phosphate flap
-
-
?
49-residue oligonucleotide duplex DNA
? + 2-deoxy-D-ribose 5-phosphate
substrate contains uracil residue at position 21. The DNA is pretreated with uracil DNA glycosylase and AP endonuclease
-
-
?
50-bp DNA containing a single abasic site preincised with AP endonuclease
29-bp DNA fragment + 2-deoxy-D-ribose 5-phosphate
-
-
-
-
?
52-pb synthetic duplex DNA
? + 2-deoxy-D-ribose 5-phosphate
labelled [32P]-uracil at position 22, pretreated with uracil DNA-glycosylase and Escherichia coli endonuclease IV
the percentage of total 2-deoxyribose 5-phosphate excised is calculated by dividing the amount of the dRP lyase product formed in each reaction by the sum of this product and the amount of the substrate DNA containing intact 5'-deoxyribose-5-phosphate
-
?
closed-circular double-stranded DNA substrate bearing a single 8-oxoguanine/cytosine base pair at a defined position
? + 2-deoxy-D-ribose 5-phosphate
-
-
-
-
?
closed-circular double-stranded DNA substrate bearing a single dihydrouracil/guanine base pair at a defined position
? + 2-deoxy-D-ribose 5-phosphate
-
-
-
-
?
DNA with a 5'-incised apurinic/apyrimidinic site at position 21
? + 2-deoxy-D-ribose 5-phosphate
-
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
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
-
?
labeled uracil-containing DNA
? + 2-deoxy-D-ribose 5-phosphate
[32P]-labeled, treated with with uracil-DNA glycosylase and apurinic/apyrimidinic endonuclease
-
-
?
mimic of a preincised DNA duplex with a 5'dRP at the site of the nick
14-mer-oligonucleotide + 2-deoxy-D-ribose 5-phosphate
-
nick substrate, containing a 3'-[32P]-labelled 16-mer with a terminal 5'-uracil, which upon pretreatment with uracil-DNA glycosylase is converted to an oligonuceotide with a 5' dRP residue, having a electrophoretic mobility of a 14.5-mer
removal of 5'dRP generates a 3'-[32P]-labelled 14-mer
-
?
preincised DNA duplex with a 5'dRP flap
15-mer-oligonucleotide + 2-deoxy-D-ribose 5-phosphate
-
flap substrate, containing a 3'-[32P]-labelled 16-mer that possesses a 5' uracil flap, which upon pretreatment with uracil-DNA glycosylase is converted to an oligonuceotide with a 5' dRP flap, having a electrophoretic mobility of a 15.5-mer
the removal of the 5' dRP generates a 3'-[32P]-labelled 15-mer
-
?
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
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
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
-
-
?
additional information
?
-
-
reaction is part of the DNA base excision repair BER
-
-
?
additional information
?
-
in addition to removal of 5'-deoxyribose phosphate from base excision repair intermediates, enzyme also removes 5'-adenylated deoxyribose phosphate from base excision repair intermediates after abortive ligation
-
-
?
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. The reaction mechanism of the lyase reaction involves a transient covalent enzyme-DNA intermediate in the form of a Schiff base connecting Lys72 of the enzyme with the 5'-dRP moiety. The Schiff base intermediate is resolved via a beta-elimination reaction, initiated by abstraction of a C2'-H atom from the 5'-deoxyribose phosphate (5'-dRP) moiety
-
-
?
additional information
?
-
-
no reaction with a DNA substrate possessing 5' uracil flap
-
-
?
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
-
-
?
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
-
-
?
additional information
?
-
-
removal of the 5'-deoxyribose phosphate group is a pivotal step in the base excision repair (BER) pathway in vivo
-
-
?
additional information
?
-
-
dRP lyase activity of the C-terminal domain of Rev1. Preparation of the 3'-end labeled dRP lyase substrate: 32P-labeled duplex DNA is pretreated with UDG and APE1 to prepare the single-nucleotide gapped substrates that contain 5'-dRP (5'-deoxyribose phosphate) flap and a 3'-OH at the margins, the S-S bond is included in the substrate molecule, overview. In vitro base excision repair (BER) activity. For kinetic analysis, a 34-bp duplex DNA substrate is prepared by annealing three DNA strands. The substrate contains an 18mer DNA strand with 6-FAM at the 3'-end and 5'-RP flap at the margin of a single-nucleotide gap
-
-
?
