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Information on EC 3.2.2.31 - adenine glycosylase and Organism(s) Escherichia coli and UniProt Accession P17802

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EC Tree
     3 Hydrolases
         3.2 Glycosylases
             3.2.2 Hydrolysing N-glycosyl compounds
                3.2.2.31 adenine glycosylase
IUBMB Comments
The enzyme serves as a mismatch repair enzyme that works to correct 7,8-dihydro-8-oxoguanine:adenine mispairs that arise in DNA when error-prone synthesis occurs past 7,8-dihydro-8-oxoguanine (GO) lesions in DNA. The enzyme excises the adenine of the mispair, producing an apurinic site sensitive to AP endonuclease activity. After removing the undamaged adenine the enzyme remains bound to the site to prevent EC 3.2.2.23 (MutM) from removing the GO lesion, which could lead to a double strand break. In vitro the enzyme is also active with adenine:guanine, adenine:cytosine, and adenine:7,8-dihydro-8-oxoadenine (AO) mispairs, removing the adenine in all cases.
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This record set is specific for:
Escherichia coli
UNIPROT: P17802
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Word Map
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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hydrolyses free adenine bases from 7,8-dihydro-8-oxoguanine:adenine mismatched double-stranded DNA, leaving an apurinic site.
Synonyms
adenine glycosylase, adenine dna glycosylase, adenine-dna glycosylase, adenine/guanine-specific dna glycosylase, a/g-specific adenine glycosylase, dna repair adenine glycosylase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
adenine DNA glycosylase
-
DNA repair adenine glycosylase
-
A/G-specific adenine glycosylase
-
-
-
-
adenine DNA glycosylase
-
-
adenine-DNA glycosylase
-
-
SYSTEMATIC NAME
IUBMB Comments
adenine-DNA deoxyribohydrolase (adenine-releasing)
The enzyme serves as a mismatch repair enzyme that works to correct 7,8-dihydro-8-oxoguanine:adenine mispairs that arise in DNA when error-prone synthesis occurs past 7,8-dihydro-8-oxoguanine (GO) lesions in DNA. The enzyme excises the adenine of the mispair, producing an apurinic site sensitive to AP endonuclease activity. After removing the undamaged adenine the enzyme remains bound to the site to prevent EC 3.2.2.23 (MutM) from removing the GO lesion, which could lead to a double strand break. In vitro the enzyme is also active with adenine:guanine, adenine:cytosine, and adenine:7,8-dihydro-8-oxoadenine (AO) mispairs, removing the adenine in all cases.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mismatch + H2O
?
show the reaction diagram
DNA containing a guanine:adenine mismatch + H2O
?
show the reaction diagram
DNA containing an adenine:7,8-dihydro-8-oxoguanine mismatch + H2O
?
show the reaction diagram
DNA containing an adenine:guanine mismatch + H2O
?
show the reaction diagram
-
-
-
?
DNA containing a 5-hydroxyuracil/adenine mismatch + H2O
?
show the reaction diagram
-
the enzyme has a moderate affinity for DNA containing a 5-hydroxyuracil/adenine mismatch
-
-
?
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mismatch + H2O
?
show the reaction diagram
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mispair + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:guanine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:thymine mismatch + H2O
?
show the reaction diagram
-
low activity
-
-
?
DNA containing a cytosine:adenine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a cytosine:adenine mispair + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a guanine:adenine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a guanine:adenine mispair + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a thymine:guanine mismatch + H2O
?
show the reaction diagram
-
low activity
-
-
?
DNA containing an adenine:7,8-dihydro-8-oxoadenine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:7,8-dihydro-8-oxoadenine mismatch + H2O
adenine + DNA with apurinic site
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:7,8-dihydro-8-oxoguanine mispair + H2O
DNA containing an abasic site + adenine
show the reaction diagram
-
primary substrate in vivo
-
-
?
DNA containing an adenine:cytosine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:guanine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:guanine mismatch + H2O
adenine + DNA with apurinic site
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mismatch + H2O
?
show the reaction diagram
DNA containing an adenine:7,8-dihydro-8-oxoguanine mismatch + H2O
?
show the reaction diagram
very high specificity
-
-
?
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mismatch + H2O
?
show the reaction diagram
DNA containing a 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mispair + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a cytosine:adenine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing a guanine:adenine mismatch + H2O
?
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:7,8-dihydro-8-oxoadenine mismatch + H2O
adenine + DNA with apurinic site
show the reaction diagram
-
-
-
-
?
DNA containing an adenine:7,8-dihydro-8-oxoguanine mispair + H2O
DNA containing an abasic site + adenine
show the reaction diagram
-
primary substrate in vivo
-
-
?
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
[4Fe-4S]-center
-
[4Fe-4S]-center
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000224
DNA containing a 5-hydroxyuracil/adenine mismatch
-
at pH 7.6 and 37°C
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000025
DNA containing a 5-hydroxyuracil/adenine mismatch
-
at pH 7.6 and 37°C
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.07
DNA containing a 5-hydroxyuracil/adenine mismatch
-
at pH 7.6 and 37°C
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme prevents DNA mutations caused by the misincorporation of adenine opposite 7,8-dihydro-8-oxo-2'-deoxyguanosine by catalyzing the deglycosylation of the aberrant adenine
physiological function
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
-
-
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
mutant enzyme C199H, hanging drop vapor diffusion method, using 1.6-1.8 M ammonium sulfate and 100 mM Tris-HCl, pH 8.5
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
C199H
the mutant shows wild type activity
C199S
the mutant shows wild type activity
D138C
the mutant shows 47% of wild type activity
D138E
the mutant shows wild type activity
D138N
inactive
E37D
the mutant shows 68% of wild type activity
K142A
the mutant shows slightly reduced activity compared to the wild type enzyme
K196A
the mutant enzyme exhibits a slight reduction of the rate of adenine removal from a G:A base pair-containing duplex compared to the wild type enzyme
K198A
the mutant enzyme exhibits a significant reduction (15fold) of the rate of adenine removal from a G:A base pair-containing duplex compared to the wild type enzyme
R194A
the mutant shows wild type activity
S120K
the mutant with bifunctional glycosylase/AP lyase activity is capable of catalyzing DNA strand scission at a rate equivalent to that of adenine excision for both guanine:adenine and 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mispair substrates
S120K/K142A
the mutant with bifunctional glycosylase/AP lyase activity is capable of catalyzing DNA strand scission at a rate equivalent to that of adenine excision for both guanine:adenine and 7,8-dihydro-8-oxo-2'-deoxyguanosine:adenine mispair substrates
D138C
-
the mutation completely inhibits the ability of the enzyme to release guanine from DNA containing a guanine:7,8-dihydro-8-oxo-2'-deoxyguanosine mismatch
D138N
-
inactive
E37C
-
the mutation still catalyzes beta- and delta-elimination reactions and can be trapped as covalent enzyme-DNA intermediates by chemical reduction
G253A
-
when 2'-deoxy-2'-fluoroadenosine in duplex paired with guanine or 7,8-dihydro-8-oxo-2'-deoxyguanosine is used, the mutant shows reduced binding affinity. Additionally, compromised glycosylase activity of the mutant enzyme is observed using the nonoptimal guanine:adenine substrate, or at low reaction temperatures
G253D
-
the mutant has a reduced adenine glycosylase activity and affinity for substrate analogues compared to the wild type enzyme
K142A
K157A
-
the mutation has no effect on enzyme activities
K158A
-
the mutation has no effect on enzyme activities
K20A
-
the mutation still catalyzes beta- and delta-elimination reactions and can be trapped as covalent enzyme-DNA intermediates by chemical reduction
Q182L
-
the mutant has significantly lower binding and glycosylase activities for adenine:guanine and adenine:7,8-dihydro-8-oxo-guanine mismatches than the wild type enzyme. The mutant has substantially increased affinity towards thymine:guanine, however, it does not exhibit any thymine/guanine or thymine/7,8-dihydro-8-oxo-guanine glycosylase activity
V45A
-
the mutant has significantly lower binding and glycosylase activities for adenine:guanine and adenine:7,8-dihydro-8-oxo-guanine mismatches than the wild type enzyme. The mutant has substantially increased affinity towards thymine:guanine, however, it does not exhibit any thymine/guanine or thymine/7,8-dihydro-8-oxo-guanine glycosylase activity
V45A/Q182L
-
the mutant has similar binding affinities to thymine/guanine as the wild type enzyme
Y82C
-
the mutant has a reduced adenine glycosylase activity and affinity for substrate analogues compared to the wild type enzyme. Additionally, compromised glycosylase activity of the mutant enzyme is observed using the nonoptimal guanine:adenine substrate, or at low reaction temperatures
Y82F
-
when 2’-deoxy-2’-fluoroadenosine in duplex paired with guanine or 7,8-dihydro-8-oxo-2'-deoxyguanosine is used, the mutant shows reduced binding affinity. Additionally, compromised glycosylase activity of the mutant enzyme is observed using the nonoptimal guanine:adenine substrate, or at low reaction temperatures
Y82L
-
the mutant is unable to discriminate between guanine and 7,8-dihydro-8-oxo-2'-deoxyguanosine when paired with 2'-deoxy-2'-fluoroadenosine
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Q-Sepharose column chromatography and HiTrap chelating column chromatography
ammonium sulfate precipitation and HiTrap heparin column chromatography
-
ammonium sulfate precipitation, phosphocellulose column chromatography, hydroxylapatite column chromatography, heparin column chromatography, and Hitrap-S column chromatography
-
heparin-Sepharose column chromatography
-
Q-Sepharose and SP-Sepharose column chromatography, and Superdex 200 gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Escherichia coli CC104 cells
-
expressed in Escherichia coli JM101 cells
-
expressed in Escherichia coli PR70(DE3) cells
-
expressed in Escherichia coli PR70/DE3 cells
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chepanoske, C.L.; Golinelli, M.P.; Williams, S.D.; David, S.S.
Positively charged residues within the iron-sulfur cluster loop of E. coli MutY participate in damage recognition and removal
Arch. Biochem. Biophys.
380
11-19
2000
Escherichia coli (P17802), Escherichia coli
Manually annotated by BRENDA team
Lu, A.L.; Lee, C.Y.; Li, L.; Li, X.
Physical and functional interactions between Escherichia coli MutY and endonuclease VIII
Biochem. J.
393
381-387
2006
Escherichia coli
Manually annotated by BRENDA team
Michaels, M.L.; Tchou, J.; Grollman, A.P.; Miller, J.H.
A repair system for 8-oxo-7,8-dihydrodeoxyguanine
Biochemistry
31
10964-10968
1992
Escherichia coli
Manually annotated by BRENDA team
Porello, S.L.; Leyes, A.E.; David, S.S.
Single-turnover and pre-steady-state kinetics of the reaction of the adenine glycosylase MutY with mismatch-containing DNA substrates
Biochemistry
37
14756-14764
1998
Escherichia coli
Manually annotated by BRENDA team
Porello, S.L.; Cannon, M.J.; David, S.S.
A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY
Biochemistry
37
6465-6475
1998
Escherichia coli
Manually annotated by BRENDA team
Williams, S.D.; David, S.S.
Formation of a Schiff base intermediate is not required for the adenine glycosylase activity of Escherichia coli MutY
Biochemistry
38
15417-15424
1999
Escherichia coli
Manually annotated by BRENDA team
Williams, S.D.; David, S.S.
A single engineered point mutation in the adenine glycosylase MutY confers bifunctional glycosylase/AP lyase activity
Biochemistry
39
10098-10109
2000
Escherichia coli (P17802), Escherichia coli
Manually annotated by BRENDA team
Messick, T.E.; Chmiel, N.H.; Golinelli, M.P.; Langer, M.R.; Joshua-Tor, L.; David, S.S.
Noncysteinyl coordination to the [4Fe-4S]2+ cluster of the DNA repair adenine glycosylase MutY introduced via site-directed mutagenesis. Structural characterization of an unusual histidinyl-coordinated cluster
Biochemistry
41
3931-3942
2002
Escherichia coli (P17802), Escherichia coli
Manually annotated by BRENDA team
Chepanoske, C.L.; Lukianova, O.A.; Lombard, M.; Golinelli-Cohen, M.P.; David, S.S.
A residue in MutY important for catalysis identified by photocross-linking and mass spectrometry
Biochemistry
43
651-662
2004
Escherichia coli
Manually annotated by BRENDA team
Livingston, A.L.; Kundu, S.; Henderson Pozzi, M.; Anderson, D.W.; David, S.S.
Insight into the roles of tyrosine 82 and glycine 253 in the Escherichia coli adenine glycosylase MutY
Biochemistry
44
14179-14190
2005
Escherichia coli
Manually annotated by BRENDA team
Chang, P.; Madabushi, A.; Lu, A.
Insights into the role of Val45 and Gln182 of Escherichia coli MutY in DNA substrate binding and specificity
BMC Biochem.
10
19
2009
Escherichia coli
Manually annotated by BRENDA team
Brinkmeyer, M.K.; Pope, M.A.; David, S.S.
Catalytic contributions of key residues in the adenine glycosylase MutY revealed by pH-dependent kinetics and cellular repair assays
Chem. Biol.
19
276-286
2012
Escherichia coli (P17802)
Manually annotated by BRENDA team
Manuel, R.C.; Czerwinski, E.W.; Lloyd, R.S.
Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme
J. Biol. Chem.
271
16218-16226
1996
Escherichia coli
Manually annotated by BRENDA team
Wright, P.M.; Yu, J.; Cillo, J.; Lu, A.L.
The active site of the Escherichia coli MutY DNA adenine glycosylase
J. Biol. Chem.
274
29011-29018
1999
Escherichia coli
Manually annotated by BRENDA team
Pope, M.A.; Porello, S.L.; David, S.S.
Escherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G A substrates
J. Biol. Chem.
277
22605-22615
2002
Escherichia coli
Manually annotated by BRENDA team
Wong, I.; Bernards, A.S.; Miller, J.K.; Wirz, J.A.
A dimeric mechanism for contextual target recognition by MutY glycosylase
J. Biol. Chem.
278
2411-2418
2003
Escherichia coli
Manually annotated by BRENDA team
Manuel, R.C.; Hitomi, K.; Arvai, A.S.; House, P.G.; Kurtz, A.J.; Dodson, M.L.; McCullough, A.K.; Tainer, J.A.; Lloyd, R.S.
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase
J. Biol. Chem.
279
46930-46939
2004
Escherichia coli
Manually annotated by BRENDA team
Volk, D.; Thiviyanathan, V.; House, P.; Lloyd, R.; Gorenstein, D.
Letter to the editor 1H, 13C and 15N resonance assignments of the C-terminal domain of MutY An adenine glycosylase active on G A mismatches
J. Biomol. NMR
14
385-386
1999
Escherichia coli
-
Manually annotated by BRENDA team
Michaels, M.L.; Pham, L.; Nghiem, Y.; Cruz, C.; Miller, J.H.
MutY, an adenine glycosylase active on G-A mispairs, has homology to endonuclease III
Nucleic Acids Res.
18
3841-3845
1990
Escherichia coli
Manually annotated by BRENDA team
Williams, S.D.; David, S.S.
Evidence that MutY is a monofunctional glycosylase capable of forming a covalent Schiff base intermediate with substrate DNA
Nucleic Acids Res.
26
5123-5133
1998
Escherichia coli
Manually annotated by BRENDA team
Chepanoske, C.L.; Porello, S.L.; Fujiwara, T.; Sugiyama, H.; David, S.S.
Substrate recognition by Escherichia coli MutY using substrate analogs
Nucleic Acids Res.
27
3197-3204
1999
Escherichia coli
Manually annotated by BRENDA team
Chmiel, N.H.; Golinelli, M.P.; Francis, A.W.; David, S.S.
Efficient recognition of substrates and substrate analogs by the adenine glycosylase MutY requires the C-terminal domain
Nucleic Acids Res.
29
553-564
2001
Escherichia coli
Manually annotated by BRENDA team
Au, K.G.; Clark, S.; Miller, J.H.; Modrich, P.
Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs
Proc. Natl. Acad. Sci. USA
86
8877-8881
1989
Escherichia coli
Manually annotated by BRENDA team
Zutterling, C.; Mursalimov, A.; Talhaoui, I.; Koshenov, Z.; Akishev, Z.; Bissenbaev, A.K.; Mazon, G.; Geacintov, N.E.; Gasparutto, D.; Groisman, R.; Zharkov, D.O.; Matkarimov, B.T.; Saparbaev, M.
Aberrant repair initiated by the adenine-DNA glycosylase does not play a role in UV-induced mutagenesis in Escherichia coli
PeerJ
6
e6029
2018
Escherichia coli
Manually annotated by BRENDA team
Tyugashev, T.; Kuznetsova, A.; Kuznetsov, N.; Fedorova, O.
Interaction features of adenine DNA glycosylase MutY from E. coli with DNA substrates
Russ. J. Bioorg. Chem.
43
13-22
2017
Escherichia coli (P17802)
-
Manually annotated by BRENDA team