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PDBsum entry 2abk
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.4.2.99.18
- DNA-(apurinic or apyrimidinic site) lyase.
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Reaction:
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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Embo J
14:4108-4120
(1995)
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PubMed id:
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Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
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M.M.Thayer,
H.Ahern,
D.Xing,
R.P.Cunningham,
J.A.Tainer.
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ABSTRACT
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The 1.85 A crystal structure of endonuclease III, combined with mutational
analysis, suggests the structural basis for the DNA binding and catalytic
activity of the enzyme. Helix-hairpin-helix (HhH) and [4Fe-4S] cluster loop
(FCL) motifs, which we have named for their secondary structure, bracket the
cleft separating the two alpha-helical domains of the enzyme. These two novel
DNA binding motifs and the solvent-filled pocket in the cleft between them all
lie within a positively charged and sequence-conserved surface region. Lys120
and Asp138, both shown by mutagenesis to be catalytically important, lie at the
mouth of this pocket, suggesting that this pocket is part of the active site.
The positions of the HhH motif and protruding FCL motif, which contains the DNA
binding residue Lys191, can accommodate B-form DNA, with a flipped-out base
bound within the active site pocket. The identification of HhH and FCL sequence
patterns in other DNA binding proteins suggests that these motifs may be a
recurrent structural theme for DNA binding proteins.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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F.Faucher,
S.S.Wallace,
and
S.Doublié
(2010).
The C-terminal lysine of Ogg2 DNA glycosylases is a major molecular determinant for guanine/8-oxoguanine distinction.
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J Mol Biol,
397,
46-56.
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PDB code:
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F.García-Prieto,
J.Gómez-Raja,
E.Andaluz,
R.Calderone,
and
G.Larriba
(2010).
Role of the homologous recombination genes RAD51 and RAD59 in the resistance of Candida albicans to UV light, radiomimetic and anti-tumor compounds and oxidizing agents.
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Fungal Genet Biol,
47,
433-445.
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G.W.Han,
X.L.Yang,
D.McMullan,
Y.E.Chong,
S.S.Krishna,
C.L.Rife,
D.Weekes,
S.M.Brittain,
P.Abdubek,
E.Ambing,
T.Astakhova,
H.L.Axelrod,
D.Carlton,
J.Caruthers,
H.J.Chiu,
T.Clayton,
L.Duan,
J.Feuerhelm,
J.C.Grant,
S.K.Grzechnik,
L.Jaroszewski,
K.K.Jin,
H.E.Klock,
M.W.Knuth,
A.Kumar,
D.Marciano,
M.D.Miller,
A.T.Morse,
E.Nigoghossian,
L.Okach,
J.Paulsen,
R.Reyes,
H.van den Bedem,
A.White,
G.Wolf,
Q.Xu,
K.O.Hodgson,
J.Wooley,
A.M.Deacon,
A.Godzik,
S.A.Lesley,
M.A.Elsliger,
P.Schimmel,
and
I.A.Wilson
(2010).
Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
66,
1326-1334.
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PDB code:
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J.C.Genereux,
A.K.Boal,
and
J.K.Barton
(2010).
DNA-mediated charge transport in redox sensing and signaling.
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J Am Chem Soc,
132,
891-905.
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L.Schomacher,
S.Smolorz,
E.Ciirdaeva,
S.Ber,
W.Kramer,
and
H.J.Fritz
(2010).
Helix-hairpin-helix protein MJ1434 from Methanocaldococcus jannaschii and EndoIV homologue TTC0482 from Thermus thermophilus HB27 do not process DNA uracil residues.
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Nucleic Acids Res,
38,
5119-5129.
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M.L.Hegde,
T.K.Hazra,
and
S.Mitra
(2010).
Functions of disordered regions in mammalian early base excision repair proteins.
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Cell Mol Life Sci,
67,
3573-3587.
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Y.G.Mok,
R.Uzawa,
J.Lee,
G.M.Weiner,
B.F.Eichman,
R.L.Fischer,
and
J.H.Huh
(2010).
Domain structure of the DEMETER 5-methylcytosine DNA glycosylase.
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Proc Natl Acad Sci U S A,
107,
19225-19230.
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A.J.Jervis,
J.C.Crack,
G.White,
P.J.Artymiuk,
M.R.Cheesman,
A.J.Thomson,
N.E.Le Brun,
and
J.Green
(2009).
The O2 sensitivity of the transcription factor FNR is controlled by Ser24 modulating the kinetics of [4Fe-4S] to [2Fe-2S] conversion.
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Proc Natl Acad Sci U S A,
106,
4659-4664.
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A.K.Boal,
J.C.Genereux,
P.A.Sontz,
J.A.Gralnick,
D.K.Newman,
and
J.K.Barton
(2009).
Redox signaling between DNA repair proteins for efficient lesion detection.
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Proc Natl Acad Sci U S A,
106,
15237-15242.
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C.Greenwood,
L.A.Selth,
A.B.Dirac-Svejstrup,
and
J.Q.Svejstrup
(2009).
An iron-sulfur cluster domain in elp3 important for the structural integrity of elongator.
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J Biol Chem,
284,
141-149.
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D.Skoko,
M.Li,
Y.Huang,
M.Mizuuchi,
M.Cai,
C.M.Bradley,
P.J.Pease,
B.Xiao,
J.F.Marko,
R.Craigie,
and
K.Mizuuchi
(2009).
Barrier-to-autointegration factor (BAF) condenses DNA by looping.
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Proc Natl Acad Sci U S A,
106,
16610-16615.
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F.W.Outten,
and
E.C.Theil
(2009).
Iron-based redox switches in biology.
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Antioxid Redox Signal,
11,
1029-1046.
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J.T.Yeeles,
R.Cammack,
and
M.S.Dillingham
(2009).
An Iron-Sulfur Cluster Is Essential for the Binding of Broken DNA by AddAB-type Helicase-Nucleases.
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J Biol Chem,
284,
7746-7755.
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K.Imamura,
S.S.Wallace,
and
S.Doublié
(2009).
Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.
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J Biol Chem,
284,
26174-26183.
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PDB codes:
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P.C.Anderson,
and
V.Daggett
(2009).
The R46Q, R131Q and R154H polymorphs of human DNA glycosylase/beta-lyase hOgg1 severely distort the active site and DNA recognition site but do not cause unfolding.
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J Am Chem Soc,
131,
9506-9515.
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S.Lee,
and
G.L.Verdine
(2009).
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.
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Proc Natl Acad Sci U S A,
106,
18497-18502.
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PDB code:
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T.Oyama,
H.Oka,
K.Mayanagi,
T.Shirai,
K.Matoba,
R.Fujikane,
Y.Ishino,
and
K.Morikawa
(2009).
Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm.
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BMC Struct Biol,
9,
2.
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PDB codes:
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A.A.Gorodetsky,
L.E.Dietrich,
P.E.Lee,
B.Demple,
D.K.Newman,
and
J.K.Barton
(2008).
DNA binding shifts the redox potential of the transcription factor SoxR.
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Proc Natl Acad Sci U S A,
105,
3684-3689.
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A.A.Gorodetsky,
M.C.Buzzeo,
and
J.K.Barton
(2008).
DNA-mediated electrochemistry.
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Bioconjug Chem,
19,
2285-2296.
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A.Ciccia,
N.McDonald,
and
S.C.West
(2008).
Structural and functional relationships of the XPF/MUS81 family of proteins.
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Annu Rev Biochem,
77,
259-287.
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A.P.Ortega-Galisteo,
T.Morales-Ruiz,
R.R.Ariza,
and
T.Roldán-Arjona
(2008).
Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks.
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Plant Mol Biol,
67,
671-681.
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G.Witte,
S.Hartung,
K.Büttner,
and
K.P.Hopfner
(2008).
Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates.
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Mol Cell,
30,
167-178.
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PDB codes:
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L.Fan,
J.O.Fuss,
Q.J.Cheng,
A.S.Arvai,
M.Hammel,
V.A.Roberts,
P.K.Cooper,
and
J.A.Tainer
(2008).
XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations.
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Cell,
133,
789-800.
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PDB codes:
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L.M.Mullen,
J.T.Bossé,
S.P.Nair,
J.M.Ward,
A.N.Rycroft,
G.Robertson,
P.R.Langford,
and
B.Henderson
(2008).
Pasteurellaceae ComE1 proteins combine the properties of fibronectin adhesins and DNA binding competence proteins.
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PLoS ONE,
3,
e3991.
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M.L.Hegde,
T.K.Hazra,
and
S.Mitra
(2008).
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
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Cell Res,
18,
27-47.
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S.C.Wolski,
J.Kuper,
P.Hänzelmann,
J.J.Truglio,
D.L.Croteau,
B.Van Houten,
and
C.Kisker
(2008).
Crystal structure of the FeS cluster-containing nucleotide excision repair helicase XPD.
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PLoS Biol,
6,
e149.
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PDB code:
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A.H.Metz,
T.Hollis,
and
B.F.Eichman
(2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
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EMBO J,
26,
2411-2420.
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PDB codes:
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A.K.Boal,
E.Yavin,
and
J.K.Barton
(2007).
DNA repair glycosylases with a [4Fe-4S] cluster: a redox cofactor for DNA-mediated charge transport?
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J Inorg Biochem,
101,
1913-1921.
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B.E.Weiner,
H.Huang,
B.M.Dattilo,
M.J.Nilges,
E.Fanning,
and
W.J.Chazin
(2007).
An iron-sulfur cluster in the C-terminal domain of the p58 subunit of human DNA primase.
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J Biol Chem,
282,
33444-33451.
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C.T.Radom,
A.Banerjee,
and
G.L.Verdine
(2007).
Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.
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J Biol Chem,
282,
9182-9194.
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PDB codes:
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D.Barthelme,
U.Scheele,
S.Dinkelaker,
A.Janoschka,
F.Macmillan,
S.V.Albers,
A.J.Driessen,
M.S.Stagni,
E.Bill,
W.Meyer-Klaucke,
V.Schünemann,
and
R.Tampé
(2007).
Structural organization of essential iron-sulfur clusters in the evolutionarily highly conserved ATP-binding cassette protein ABCE1.
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J Biol Chem,
282,
14598-14607.
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J.Timmins,
I.Leiros,
and
S.McSweeney
(2007).
Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding.
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EMBO J,
26,
3260-3271.
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PDB code:
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J.Y.Ha,
H.K.Kim,
d.o. .J.Kim,
K.H.Kim,
S.J.Oh,
H.H.Lee,
H.J.Yoon,
H.K.Song,
and
S.W.Suh
(2007).
The recombination-associated protein RdgC adopts a novel toroidal architecture for DNA binding.
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Nucleic Acids Res,
35,
2671-2681.
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PDB code:
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K.Singh,
A.Srivastava,
S.S.Patel,
and
M.J.Modak
(2007).
Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA.
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J Biol Chem,
282,
10594-10604.
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M.L.Mendillo,
C.D.Putnam,
and
R.D.Kolodner
(2007).
Escherichia coli MutS tetramerization domain structure reveals that stable dimers but not tetramers are essential for DNA mismatch repair in vivo.
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J Biol Chem,
282,
16345-16354.
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PDB code:
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T.K.Hazra,
A.Das,
S.Das,
S.Choudhury,
Y.W.Kow,
and
R.Roy
(2007).
Oxidative DNA damage repair in mammalian cells: a new perspective.
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DNA Repair (Amst),
6,
470-480.
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J.Rudolf,
V.Makrantoni,
W.J.Ingledew,
M.J.Stark,
and
M.F.White
(2006).
The DNA repair helicases XPD and FancJ have essential iron-sulfur domains.
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Mol Cell,
23,
801-808.
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M.Honda,
J.Inoue,
M.Yoshimasu,
Y.Ito,
T.Shibata,
and
T.Mikawa
(2006).
Identification of the RecR Toprim domain as the binding site for both RecF and RecO. A role of RecR in RecFOR assembly at double-stranded DNA-single-stranded DNA junctions.
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J Biol Chem,
281,
18549-18559.
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G.M.Lingaraju,
A.A.Sartori,
D.Kostrewa,
A.E.Prota,
J.Jiricny,
and
F.K.Winkler
(2005).
A DNA glycosylase from Pyrobaculum aerophilum with an 8-oxoguanine binding mode and a noncanonical helix-hairpin-helix structure.
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Structure,
13,
87-98.
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PDB codes:
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M.Newman,
J.Murray-Rust,
J.Lally,
J.Rudolf,
A.Fadden,
P.P.Knowles,
M.F.White,
and
N.Q.McDonald
(2005).
Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition.
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EMBO J,
24,
895-905.
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PDB codes:
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N.A.Kuznetsov,
V.V.Koval,
D.O.Zharkov,
G.A.Nevinsky,
K.T.Douglas,
and
O.S.Fedorova
(2005).
Kinetics of substrate recognition and cleavage by human 8-oxoguanine-DNA glycosylase.
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Nucleic Acids Res,
33,
3919-3931.
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O.A.Lukianova,
and
S.S.David
(2005).
A role for iron-sulfur clusters in DNA repair.
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Curr Opin Chem Biol,
9,
145-151.
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T.Nishino,
K.Komori,
Y.Ishino,
and
K.Morikawa
(2005).
Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms.
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Structure,
13,
1183-1192.
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PDB code:
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T.Watanabe,
J.O.Blaisdell,
S.S.Wallace,
and
J.P.Bond
(2005).
Engineering functional changes in Escherichia coli endonuclease III based on phylogenetic and structural analyses.
|
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J Biol Chem,
280,
34378-34384.
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A.Das,
L.Rajagopalan,
V.S.Mathura,
S.J.Rigby,
S.Mitra,
and
T.K.Hazra
(2004).
Identification of a zinc finger domain in the human NEIL2 (Nei-like-2) protein.
|
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J Biol Chem,
279,
47132-47138.
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PDB code:
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B.I.Lee,
K.H.Kim,
S.J.Park,
S.H.Eom,
H.K.Song,
and
S.W.Suh
(2004).
Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair.
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| |
EMBO J,
23,
2029-2038.
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PDB code:
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H.Zhao,
and
P.Russell
(2004).
DNA binding domain in the replication checkpoint protein Mrc1 of Schizosaccharomyces pombe.
|
| |
J Biol Chem,
279,
53023-53027.
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J.Brozmanová,
V.Vlcková,
and
M.Chovanec
(2004).
How heterologously expressed Escherichia coli genes contribute to understanding DNA repair processes in Saccharomyces cerevisiae.
|
| |
Curr Genet,
46,
317-330.
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J.C.Fromme,
A.Banerjee,
and
G.L.Verdine
(2004).
DNA glycosylase recognition and catalysis.
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Curr Opin Struct Biol,
14,
43-49.
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Y.Choi,
J.J.Harada,
R.B.Goldberg,
and
R.L.Fischer
(2004).
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene.
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| |
Proc Natl Acad Sci U S A,
101,
7481-7486.
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B.F.Eichman,
E.J.O'Rourke,
J.P.Radicella,
and
T.Ellenberger
(2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
|
| |
EMBO J,
22,
4898-4909.
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PDB codes:
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B.R.Szymczyna,
J.Bowman,
S.McCracken,
A.Pineda-Lucena,
Y.Lu,
B.Cox,
M.Lambermon,
B.R.Graveley,
C.H.Arrowsmith,
and
B.J.Blencowe
(2003).
Structure and function of the PWI motif: a novel nucleic acid-binding domain that facilitates pre-mRNA processing.
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| |
Genes Dev,
17,
461-475.
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PDB code:
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D.S.Shin,
L.Pellegrini,
D.S.Daniels,
B.Yelent,
L.Craig,
D.Bates,
D.S.Yu,
M.K.Shivji,
C.Hitomi,
A.S.Arvai,
N.Volkmann,
H.Tsuruta,
T.L.Blundell,
A.R.Venkitaraman,
and
J.A.Tainer
(2003).
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2.
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| |
EMBO J,
22,
4566-4576.
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PDB code:
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E.J.O'Rourke,
C.Chevalier,
A.V.Pinto,
J.M.Thiberge,
L.Ielpi,
A.Labigne,
and
J.P.Radicella
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Cell,
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Nat Struct Biol,
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PDB code:
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D.J.Hosfield,
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Cell,
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PDB code:
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D.O.Zharkov,
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PDB codes:
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M.Tani,
K.Shinmura,
T.Kohno,
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
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PDB code:
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PDB codes:
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The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome.
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Nat Struct Biol,
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PDB code:
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G.P.Mullen,
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DNA polymerase beta in abasic site repair: a structurally conserved helix-hairpin-helix motif in lesion detection by base excision repair enzymes.
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Biochemistry,
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Biochemistry,
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PDB codes:
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O.D.Schärer,
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Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors.
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Biochemistry,
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Cloning and characterization of a mammalian 8-oxoguanine DNA glycosylase.
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Proc Natl Acad Sci U S A,
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Cloning and expression of the cDNA encoding the human homologue of the DNA repair enzyme, Escherichia coli endonuclease III.
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Molecular cloning and functional expression of a human cDNA encoding the antimutator enzyme 8-hydroxyguanine-DNA glycosylase.
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PDB codes:
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
|
|
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