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PDBsum entry 2abk

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Endonuclease PDB id
2abk
Jmol
Contents
Protein chain
211 a.a. *
Ligands
SF4
Waters ×123
* Residue conservation analysis
PDB id:
2abk
Name: Endonuclease
Title: Refinement of the native structure of endonuclease iii to a resolution of 1.85 angstrom
Structure: Endonuclease iii. Chain: a. Ec: 4.2.99.18
Source: Escherichia coli. Organism_taxid: 562. Strain: uc 6444 delta nth
Resolution:
1.85Å     R-factor:   0.185     R-free:   0.216
Authors: M.M.Thayer,J.A.Tainer
Key ref: M.M.Thayer et al. (1995). Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J, 14, 4108-4120. PubMed id: 7664751
Date:
11-May-95     Release date:   15-Oct-95    
Supersedes: 1abk
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AB83  (END3_ECOLI) -  Endonuclease III
Seq:
Struc:
211 a.a.
211 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
EMBO J 14:4108-4120 (1995)
PubMed id: 7664751  
 
 
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
M.M.Thayer, H.Ahern, D.Xing, R.P.Cunningham, J.A.Tainer.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20083120 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.
  J Mol Biol, 397, 46-56.
PDB code: 3knt
20206282 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.
  Fungal Genet Biol, 47, 433-445.  
  20944229 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.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1326-1334.
PDB code: 2g36
20047321 J.C.Genereux, A.K.Boal, and J.K.Barton (2010).
DNA-mediated charge transport in redox sensing and signaling.
  J Am Chem Soc, 132, 891-905.  
20410075 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.
  Nucleic Acids Res, 38, 5119-5129.  
20714778 M.L.Hegde, T.K.Hazra, and S.Mitra (2010).
Functions of disordered regions in mammalian early base excision repair proteins.
  Cell Mol Life Sci, 67, 3573-3587.  
20974931 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.
  Proc Natl Acad Sci U S A, 107, 19225-19230.  
19261852 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.
  Proc Natl Acad Sci U S A, 106, 4659-4664.  
19720997 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.
  Proc Natl Acad Sci U S A, 106, 15237-15242.  
18986986 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.
  J Biol Chem, 284, 141-149.  
19805345 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.
  Proc Natl Acad Sci U S A, 106, 16610-16615.  
19021503 F.W.Outten, and E.C.Theil (2009).
Iron-based redox switches in biology.
  Antioxid Redox Signal, 11, 1029-1046.  
19129187 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.
  J Biol Chem, 284, 7746-7755.  
19625256 K.Imamura, S.S.Wallace, and S.Doublié (2009).
Structural characterization of a viral NEIL1 ortholog unliganded and bound to abasic site-containing DNA.
  J Biol Chem, 284, 26174-26183.
PDB codes: 3a42 3a45 3a46
19537786 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.
  J Am Chem Soc, 131, 9506-9515.  
19841264 S.Lee, and G.L.Verdine (2009).
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.
  Proc Natl Acad Sci U S A, 106, 18497-18502.
PDB code: 3g0q
19159486 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.
  BMC Struct Biol, 9, 2.
PDB codes: 2zj2 2zj5 2zj8 2zja
18316718 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.
  Proc Natl Acad Sci U S A, 105, 3684-3689.  
18980370 A.A.Gorodetsky, M.C.Buzzeo, and J.K.Barton (2008).
DNA-mediated electrochemistry.
  Bioconjug Chem, 19, 2285-2296.  
18518821 A.Ciccia, N.McDonald, and S.C.West (2008).
Structural and functional relationships of the XPF/MUS81 family of proteins.
  Annu Rev Biochem, 77, 259-287.  
18493721 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.
  Plant Mol Biol, 67, 671-681.  
18439896 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.
  Mol Cell, 30, 167-178.
PDB codes: 3c1y 3c1z 3c21 3c23
18510924 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.
  Cell, 133, 789-800.
PDB codes: 3crv 3crw
19098981 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.
  PLoS ONE, 3, e3991.  
18166975 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.
  Cell Res, 18, 27-47.  
18578568 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.
  PLoS Biol, 6, e149.
PDB code: 2vsf
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17599416 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?
  J Inorg Biochem, 101, 1913-1921.  
17893144 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.
  J Biol Chem, 282, 33444-33451.  
17114185 C.T.Radom, A.Banerjee, and G.L.Verdine (2007).
Structural characterization of human 8-oxoguanine DNA glycosylase variants bearing active site mutations.
  J Biol Chem, 282, 9182-9194.
PDB codes: 2nob 2noe 2nof 2noh 2noi 2nol 2noz
17355973 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.
  J Biol Chem, 282, 14598-14607.  
17581636 J.Timmins, I.Leiros, and S.McSweeney (2007).
Crystal structure and mutational study of RecOR provide insight into its mode of DNA binding.
  EMBO J, 26, 3260-3271.
PDB code: 2v1c
17426134 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.
  Nucleic Acids Res, 35, 2671-2681.
PDB code: 2owy
17259182 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.
  J Biol Chem, 282, 10594-10604.  
17426027 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.
  J Biol Chem, 282, 16345-16354.
PDB code: 2ok2
17116430 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.
  DNA Repair (Amst), 6, 470-480.  
16973432 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.
  Mol Cell, 23, 801-808.  
16675461 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.
  J Biol Chem, 281, 18549-18559.  
15642264 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.
  Structure, 13, 87-98.
PDB codes: 1xqo 1xqp
15719018 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.
  EMBO J, 24, 895-905.
PDB codes: 2bgw 2bhn
16024742 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.
  Nucleic Acids Res, 33, 3919-3931.  
15811798 O.A.Lukianova, and S.S.David (2005).
A role for iron-sulfur clusters in DNA repair.
  Curr Opin Chem Biol, 9, 145-151.  
16084390 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.
  Structure, 13, 1183-1192.
PDB code: 1x2i
16096281 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.
  J Biol Chem, 280, 34378-34384.  
15339932 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.
  J Biol Chem, 279, 47132-47138.
PDB code: 1vzp
15116069 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.
  EMBO J, 23, 2029-2038.
PDB code: 1vdd
15471884 H.Zhao, and P.Russell (2004).
DNA binding domain in the replication checkpoint protein Mrc1 of Schizosaccharomyces pombe.
  J Biol Chem, 279, 53023-53027.  
15614491 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.  
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
15128940 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.
  Proc Natl Acad Sci U S A, 101, 7481-7486.  
14517230 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.
PDB codes: 1pu6 1pu7 1pu8
12600940 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.
  Genes Dev, 17, 461-475.
PDB code: 1mp1
12941707 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.
  EMBO J, 22, 4566-4576.
PDB code: 1pzn
12601164 E.J.O'Rourke, C.Chevalier, A.V.Pinto, J.M.Thiberge, L.Ielpi, A.Labigne, and J.P.Radicella (2003).
Pathogen DNA as target for host-generated oxidative stress: role for repair of bacterial DNA damage in Helicobacter pylori colonization.
  Proc Natl Acad Sci U S A, 100, 2789-2794.  
14559969 E.M.Boon, A.L.Livingston, N.H.Chmiel, S.S.David, and J.K.Barton (2003).
DNA-mediated charge transport for DNA repair.
  Proc Natl Acad Sci U S A, 100, 12543-12547.  
14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
  Annu Rev Biochem, 72, 337-366.  
14522990 H.Dou, S.Mitra, and T.K.Hazra (2003).
Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2.
  J Biol Chem, 278, 49679-49684.  
12840008 J.C.Fromme, and G.L.Verdine (2003).
Structure of a trapped endonuclease III-DNA covalent intermediate.
  EMBO J, 22, 3461-3471.
PDB codes: 1orn 1orp 1p59
12592398 J.C.Fromme, S.D.Bruner, W.Yang, M.Karplus, and G.L.Verdine (2003).
Product-assisted catalysis in base-excision DNA repair.
  Nat Struct Biol, 10, 204-211.
PDB codes: 1hu0 1lwv 1lww 1lwy
12682355 J.H.Chung, E.K.Im, H.Y.Park, J.H.Kwon, S.Lee, J.Oh, K.C.Hwang, J.H.Lee, and Y.Jang (2003).
A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily.
  Nucleic Acids Res, 31, 2045-2055.  
12456671 P.Wu, C.Qiu, A.Sohail, X.Zhang, A.S.Bhagwat, and X.Cheng (2003).
Mismatch repair in methylated DNA. Structure and activity of the mismatch-specific thymine glycosylase domain of methyl-CpG-binding protein MBD4.
  J Biol Chem, 278, 5285-5291.
PDB code: 1ngn
12668677 R.J.O'Neill, O.V.Vorob'eva, H.Shahbakhti, E.Zmuda, A.S.Bhagwat, and G.S.Baldwin (2003).
Mismatch uracil glycosylase from Escherichia coli: a general mismatch or a specific DNA glycosylase?
  J Biol Chem, 278, 20526-20532.  
14522981 X.Liu, S.Choudhury, and R.Roy (2003).
In vitro and in vivo dimerization of human endonuclease III stimulates its activity.
  J Biol Chem, 278, 50061-50069.  
12368475 A.R.Pavlov, G.I.Belova, S.A.Kozyavkin, and A.I.Slesarev (2002).
Helix-hairpin-helix motifs confer salt resistance and processivity on chimeric DNA polymerases.
  Proc Natl Acad Sci U S A, 99, 13510-13515.  
12057763 D.O.Zharkov, and A.P.Grollman (2002).
Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases.
  Free Radic Biol Med, 32, 1254-1263.  
11847126 D.O.Zharkov, G.Golan, R.Gilboa, A.S.Fernandes, S.E.Gerchman, J.H.Kycia, R.A.Rieger, A.P.Grollman, and G.Shoham (2002).
Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
  EMBO J, 21, 789-800.
PDB codes: 1k3w 1k3x
11733530 G.I.Belova, R.Prasad, I.V.Nazimov, S.H.Wilson, and A.I.Slesarev (2002).
The domain organization and properties of individual domains of DNA topoisomerase V, a type 1B topoisomerase with DNA repair activities.
  J Biol Chem, 277, 4959-4965.  
11877410 J.A.Hinks, M.C.Evans, Y.De Miguel, A.A.Sartori, J.Jiricny, and L.H.Pearl (2002).
An iron-sulfur cluster in the family 4 uracil-DNA glycosylases.
  J Biol Chem, 277, 16936-16940.  
12084915 J.J.Dervan, M.Feng, D.Patel, J.A.Grasby, P.J.Artymiuk, T.A.Ceska, and J.R.Sayers (2002).
Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding.
  Proc Natl Acad Sci U S A, 99, 8542-8547.
PDB code: 1j5f
12198481 K.S.Yan, and M.M.Zhou (2002).
TAGging the target for damage control.
  Nat Struct Biol, 9, 638-640.  
12065399 L.Serre, K.Pereira de Jésus, S.Boiteux, C.Zelwer, and B.Castaing (2002).
Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
  EMBO J, 21, 2854-2865.
PDB codes: 1kfv 7abc
12167705 M.T.Ocampo, W.Chaung, D.R.Marenstein, M.K.Chan, A.Altamirano, A.K.Basu, R.J.Boorstein, R.P.Cunningham, and G.W.Teebor (2002).
Targeted deletion of mNth1 reveals a novel DNA repair enzyme activity.
  Mol Cell Biol, 22, 6111-6121.  
12093749 M.Takao, S.Kanno, T.Shiromoto, R.Hasegawa, H.Ide, S.Ikeda, A.H.Sarker, S.Seki, J.Z.Xing, X.C.Le, M.Weinfeld, K.Kobayashi, J.Miyazaki, M.Muijtjens, J.H.Hoeijmakers, G.van der Horst, A.Yasui, and A.H.Sarker (2002).
Novel nuclear and mitochondrial glycosylases revealed by disruption of the mouse Nth1 gene encoding an endonuclease III homolog for repair of thymine glycols.
  EMBO J, 21, 3486-3493.  
11912217 R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, and G.Shoham (2002).
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
  J Biol Chem, 277, 19811-19816.
PDB code: 1k82
12401779 R.H.Elder, and G.L.Dianov (2002).
Repair of dihydrouracil supported by base excision repair in mNTH1 knock-out cell extracts.
  J Biol Chem, 277, 50487-50490.  
12426397 S.Singh, G.E.Folkers, A.M.Bonvin, R.Boelens, R.Wechselberger, A.Niztayev, and R.Kaptein (2002).
Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli.
  EMBO J, 21, 6257-6266.
PDB code: 1kft
12000829 V.Starkuviene, and H.J.Fritz (2002).
A novel type of uracil-DNA glycosylase mediating repair of hydrolytic DNA damage in the extremely thermophilic eubacterium Thermus thermophilus.
  Nucleic Acids Res, 30, 2097-2102.  
11788726 Y.N.Fondufe-Mittendorf, C.Härer, W.Kramer, and H.J.Fritz (2002).
Two amino acid replacements change the substrate preference of DNA mismatch glycosylase Mig.MthI from T/G to A/G.
  Nucleic Acids Res, 30, 614-621.  
12361800 Y.W.Kow (2002).
Repair of deaminated bases in DNA.
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11267993 A.Bellacosa (2001).
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11087375 C.V.Privezentzev, M.Saparbaev, A.Sambandam, M.M.Greenberg, and J.Laval (2000).
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PDB codes: 1dgs 1dgt 1v9p
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DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
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Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
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Purification and characterization of Thermotoga maritima endonuclease IV, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase.
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The active site of the Escherichia coli MutY DNA adenine glycosylase.
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Envisioning the molecular choreography of DNA base excision repair.
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A new member of the endonuclease III family of DNA repair enzymes that removes methylated purines from DNA.
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PDB code: 2irf
10571185 Y.X.Wang, N.Neamati, J.Jacob, I.Palmer, S.J.Stahl, J.D.Kaufman, P.L.Huang, P.L.Huang, H.E.Winslow, Y.Pommier, P.T.Wingfield, S.Lee-Huang, A.Bax, and D.A.Torchia (1999).
Solution structure of anti-HIV-1 and anti-tumor protein MAP30: structural insights into its multiple functions.
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Characterization of the recombinant MutY homolog, an adenine DNA glycosylase, from yeast Schizosaccharomyces pombe.
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Crystal structure of E.coli RuvA with bound DNA Holliday junction at 6 A resolution.
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PDB code: 1bdx
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Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.
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MutY DNA glycosylase: base release and intermediate complex formation.
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Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
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PDB codes: 7mht 8mht 9mht
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Base flipping.
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Functional analysis of the amino-terminal 8-kDa domain of DNA polymerase beta as revealed by site-directed mutagenesis. DNA binding and 5'-deoxyribose phosphate lyase activities.
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Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.
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Spore photoproduct lyase from Bacillus subtilis spores is a novel iron-sulfur DNA repair enzyme which shares features with proteins such as class III anaerobic ribonucleotide reductases and pyruvate-formate lyases.
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Repair of oxidatively damaged guanine in Saccharomyces cerevisiae by an alternative pathway.
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Purification and characterization of human NTH1, a homolog of Escherichia coli endonuclease III. Direct identification of Lys-212 as the active nucleophilic residue.
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A substrate recognition role for the [4Fe-4S]2+ cluster of the DNA repair glycosylase MutY.
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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 codes: 1akz 1ssp 2ssp
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A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
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PDB code: 1bmy
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MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily.
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PDB codes: 1mud 1mun 1muy
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Catalytic center of DNA polymerase beta for excision of deoxyribose phosphate groups.
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Protein folds in the all-beta and all-alpha classes.
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DNA-repair enzymes.
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Insights into the mechanisms of homologous recombination from the structure of RuvA.
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Kinetics of oxidized cytosine repair by endonuclease III of Escherichia coli.
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9302998 G.Musco, A.Kharrat, G.Stier, F.Fraternali, T.J.Gibson, M.Nilges, and A.Pastore (1997).
The solution structure of the first KH domain of FMR1, the protein responsible for the fragile X syndrome.
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PDB code: 2fmr
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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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Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
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Charge density-dependent strength of hydration and biological structure.
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9020769 L.Augeri, Y.M.Lee, A.B.Barton, and P.W.Doetsch (1997).
Purification, characterization, gene cloning, and expression of Saccharomyces cerevisiae redoxyendonuclease, a homolog of Escherichia coli endonuclease III.
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Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis.
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9321410 M.Bjorâs, L.Luna, B.Johnsen, E.Hoff, T.Haug, T.Rognes, and E.Seeberg (1997).
Opposite base-dependent reactions of a human base excision repair enzyme on DNA containing 7,8-dihydro-8-oxoguanine and abasic sites.
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Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism.
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PDB codes: 1bpx 1bpy 1bpz
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Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors.
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Prokaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.
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The Ogg1 protein of Saccharomyces cerevisiae: a 7,8-dihydro-8-oxoguanine DNA glycosylase/AP lyase whose lysine 241 is a critical residue for catalytic activity.
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Cloning and characterization of a functional human homolog of Escherichia coli endonuclease III.
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9287157 R.C.Manuel, and R.S.Lloyd (1997).
Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
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A mammalian DNA repair enzyme that excises oxidatively damaged guanines maps to a locus frequently lost in lung cancer.
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Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
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Cloning and characterization of a mammalian 8-oxoguanine DNA glycosylase.
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DNA excision repair pathways.
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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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Specific recognition of A/G and A/7,8-dihydro-8-oxoguanine (8-oxoG) mismatches by Escherichia coli MutY: removal of the C-terminal domain preferentially affects A/8-oxoG recognition.
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Catalytic mechanism and DNA substrate recognition of Escherichia coli MutY protein.
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A novel family of phospholipase D homologues that includes phospholipid synthases and putative endonucleases: identification of duplicated repeats and potential active site residues.
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Activation of SoxR-dependent transcription in vitro by noncatalytic or NifS-mediated assembly of [2Fe-2S] clusters into apo-SoxR.
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Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily.
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Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, processivity, and fidelity.
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PDB codes: 9icm 9icw 9icx 9icy
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Counteracting the mutagenic effect of hydrolytic deamination of DNA 5-methylcytosine residues at high temperature: DNA mismatch N-glycosylase Mig.Mth of the thermophilic archaeon Methanobacterium thermoautotrophicum THF.
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8855249 L.Eide, M.Bjørås, M.Pirovano, I.Alseth, K.G.Berdal, and E.Seeberg (1996).
Base excision of oxidative purine and pyrimidine DNA damage in Saccharomyces cerevisiae by a DNA glycosylase with sequence similarity to endonuclease III from Escherichia coli.
  Proc Natl Acad Sci U S A, 93, 10735-10740.  
8663135 R.C.Manuel, E.W.Czerwinski, and R.S.Lloyd (1996).
Identification of the structural and functional domains of MutY, an Escherichia coli DNA mismatch repair enzyme.
  J Biol Chem, 271, 16218-16226.  
8611553 T.P.Hilbert, R.J.Boorstein, H.C.Kung, P.H.Bolton, D.Xing, R.P.Cunningham, and G.W.Teebor (1996).
Purification of a mammalian homologue of Escherichia coli endonuclease III: identification of a bovine pyrimidine hydrate-thymine glycol DNAse/AP lyase by irreversible cross linking to a thymine glycol-containing oligoxynucleotide.
  Biochemistry, 35, 2505-2511.  
8811082 T.Roldán-Arjona, C.Anselmino, and T.Lindahl (1996).
Molecular cloning and functional analysis of a Schizosaccharomyces pombe homologue of Escherichia coli endonuclease III.
  Nucleic Acids Res, 24, 3307-3312.  
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