spacer
spacer

PDBsum entry 1ako

Go to PDB code: 
protein links
Nuclease PDB id
1ako
Jmol
Contents
Protein chain
268 a.a. *
Waters ×190
* Residue conservation analysis
PDB id:
1ako
Name: Nuclease
Title: Exonuclease iii from escherichia coli
Structure: Exonuclease iii. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cell_line: bl21. Gene: xth. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Monomer (from PDB file)
Resolution:
1.70Å     R-factor:   0.169     R-free:   0.202
Authors: C.D.Mol,C.-F.Kuo,M.M.Thayer,R.P.Cunningham,J.A.Tainer
Key ref: C.D.Mol et al. (1995). Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature, 374, 381-386. PubMed id: 7885481
Date:
26-May-97     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09030  (EX3_ECOLI) -  Exodeoxyribonuclease III
Seq:
Struc:
268 a.a.
268 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.11.2  - Exodeoxyribonuclease Iii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Degradation of double-stranded DNA. It acts progressively in a 3'- to 5'-direction, releasing nucleoside 5'-phosphates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     nucleic acid phosphodiester bond hydrolysis   6 terms 
  Biochemical function     hydrolase activity     9 terms  

 

 
Nature 374:381-386 (1995)
PubMed id: 7885481  
 
 
Structure and function of the multifunctional DNA-repair enzyme exonuclease III.
C.D.Mol, C.F.Kuo, M.M.Thayer, R.P.Cunningham, J.A.Tainer.
 
  ABSTRACT  
 
The repair of DNA requires the removal of abasic sites, which are constantly generated in vivo both spontaneously and by enzymatic removal of uracil, and of bases damaged by active oxygen species, alkylating agents and ionizing radiation. The major apurinic/apyrimidinic (AP) DNA-repair endonuclease in Escherichia coli is the multifunctional enzyme exonuclease III, which also exhibits 3'-repair diesterase, 3'-->5' exonuclease, 3'-phosphomonoesterase and ribonuclease activities. We report here the 1.7 A resolution crystal structure of exonuclease III which reveals a 2-fold symmetric, four-layered alpha beta fold with similarities to both deoxyribonuclease I and RNase H. In the ternary complex determined at 2.6 A resolution, Mn2+ and dCMP bind to exonuclease III at one end of the alpha beta-sandwich, in a region dominated by positive electrostatic potential. Residues conserved among AP endonucleases from bacteria to man cluster within this active site and appear to participate in phosphate-bond cleavage at AP sites through a nucleophilic attack facilitated by a single bound metal ion.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21245038 J.B.Poulsen, K.R.Andersen, K.H.Kjær, F.Durand, P.Faou, A.L.Vestergaard, G.H.Talbo, N.Hoogenraad, D.E.Brodersen, J.Justesen, and P.M.Martensen (2011).
Human 2'-phosphodiesterase localizes to the mitochondrial matrix with a putative function in mitochondrial RNA turnover.
  Nucleic Acids Res, 39, 3754-3770.  
21266972 M.Z.Mohammed, V.N.Vyjayanti, C.A.Laughton, L.V.Dekker, P.M.Fischer, D.M.Wilson, R.Abbotts, S.Shah, P.M.Patel, I.D.Hickson, and S.Madhusudan (2011).
Development and evaluation of human AP endonuclease inhibitors in melanoma and glioma cell lines.
  Br J Cancer, 104, 653-663.  
21305083 M.Zhang, Y.M.Guan, and B.C.Ye (2011).
Ultrasensitive fluorescence polarization DNA detection by target assisted exonuclease III-catalyzed signal amplification.
  Chem Commun (Camb), 47, 3478-3480.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20616014 P.A.Nair, P.Smith, and S.Shuman (2010).
Structure of bacterial LigD 3'-phosphoesterase unveils a DNA repair superfamily.
  Proc Natl Acad Sci U S A, 107, 12822-12827.
PDB codes: 3n9b 3n9d
20056333 R.Abbotts, and S.Madhusudan (2010).
Human AP endonuclease 1 (APE1): from mechanistic insights to druggable target in cancer.
  Cancer Treat Rev, 36, 425-435.  
20444876 R.Potestio, T.Aleksiev, F.Pontiggia, S.Cozzini, and C.Micheletti (2010).
ALADYN: a web server for aligning proteins by matching their large-scale motion.
  Nucleic Acids Res, 38, W41-W45.  
19484131 A.Simeonov, A.Kulkarni, D.Dorjsuren, A.Jadhav, M.Shen, D.R.McNeill, C.P.Austin, and D.M.Wilson (2009).
Identification and characterization of inhibitors of human apurinic/apyrimidinic endonuclease APE1.
  PLoS One, 4, e5740.  
18561002 H.Kurita, K.Torii, H.Yasuda, K.Takashima, S.Katsura, and A.Mizuno (2009).
The effect of physical form of DNA on exonucleaseIII activity revealed by single-molecule observations.
  J Fluoresc, 19, 33-40.  
  19462533 J.Ahn, M.V.Poyurovsky, N.Baptiste, R.Beckerman, C.Cain, M.Mattia, K.McKinney, J.Zhou, A.Zupnick, V.Gottifredi, and C.Prives (2009).
Dissection of the sequence-specific DNA binding and exonuclease activities reveals a superactive yet apoptotically impaired mutant p53 protein.
  Cell Cycle, 8, 1603-1615.  
19350599 J.Zhu, Y.Zhao, Y.Zhu, Z.Wu, M.Lin, W.He, Y.Wang, G.Chen, L.Dong, J.Zhang, Y.Lu, and Z.Guo (2009).
DNA cross-linking patterns induced by an antitumor-active trinuclear platinum complex and comparison with its dinuclear analogue.
  Chemistry, 15, 5245-5253.  
19318463 N.L.Ernst, B.Panicucci, J.Carnes, and K.Stuart (2009).
Differential functions of two editosome exoUases in Trypanosoma brucei.
  RNA, 15, 947-957.  
19527659 R.Potestio, F.Pontiggia, and C.Micheletti (2009).
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.
  Biophys J, 96, 4993-5002.  
19201803 T.Zimmermann, T.Sorg, S.Y.Siehler, and U.Gerischer (2009).
Role of Acinetobacter baylyi Crc in catabolite repression of enzymes for aromatic compound catabolism.
  J Bacteriol, 191, 2834-2842.  
18576638 A.S.Lipton, R.W.Heck, S.Primak, D.R.McNeill, D.M.Wilson, and P.D.Ellis (2008).
Characterization of Mg2+ binding to the DNA repair protein apurinic/apyrimidic endonuclease 1 via solid-state 25Mg NMR spectroscopy.
  J Am Chem Soc, 130, 9332-9341.  
18369194 A.Zen, V.Carnevale, A.M.Lesk, and C.Micheletti (2008).
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.
  Protein Sci, 17, 918-929.  
18439621 B.R.Berquist, D.R.McNeill, and D.M.Wilson (2008).
Characterization of abasic endonuclease activity of human Ape1 on alternative substrates, as well as effects of ATP and sequence context on AP site incision.
  J Mol Biol, 379, 17-27.  
18766469 L.Rittié, and B.Perbal (2008).
Enzymes used in molecular biology: a useful guide.
  J Cell Commun Signal, 2, 25-45.  
18055191 Y.Zhang, H.Zhang, and N.Hu (2008).
Using exonuclease III to enhance electrochemical detection of natural DNA damage in layered films.
  Biosens Bioelectron, 23, 1077-1082.  
17318183 E.P.Carpenter, A.Corbett, H.Thomson, J.Adacha, K.Jensen, J.Bergeron, I.Kasampalidis, R.Exley, M.Winterbotham, C.Tang, G.S.Baldwin, and P.Freemont (2007).
AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis.
  EMBO J, 26, 1363-1372.
PDB codes: 2jc4 2jc5
17699520 K.Rogers, G.Gao, and L.Simpson (2007).
Uridylate-specific 3' 5'-exoribonucleases involved in uridylate-deletion RNA editing in trypanosomatid mitochondria.
  J Biol Chem, 282, 29073-29080.  
17138564 M.Ghosh, G.Meiss, A.M.Pingoud, R.E.London, and L.C.Pedersen (2007).
The nuclease a-inhibitor complex is characterized by a novel metal ion bridge.
  J Biol Chem, 282, 5682-5690.
PDB code: 2o3b
17567612 M.R.Hodskinson, L.M.Allen, D.P.Thomson, and J.R.Sayers (2007).
Molecular interactions of Escherichia coli ExoIX and identification of its associated 3'-5' exonuclease activity.
  Nucleic Acids Res, 35, 4094-4102.  
17576692 S.Nakanishi, R.Prasad, S.H.Wilson, and M.Smerdon (2007).
Different structural states in oligonucleosomes are required for early versus late steps of base excision repair.
  Nucleic Acids Res, 35, 4313-4321.  
16505354 E.Yavin, E.D.Stemp, V.L.O'shea, S.S.David, and J.K.Barton (2006).
Electron trap for DNA-bound repair enzymes: a strategy for DNA-mediated signaling.
  Proc Natl Acad Sci U S A, 103, 3610-3614.  
16595670 H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, and J.Sakurai (2006).
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
  J Biol Chem, 281, 16157-16167.
PDB codes: 2ddr 2dds 2ddt
16780580 I.S.Mian, E.A.Worthey, and R.Salavati (2006).
Taking U out, with two nucleases?
  BMC Bioinformatics, 7, 305.  
16540594 K.Kaneda, J.Sekiguchi, and T.Shida (2006).
Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism.
  Nucleic Acids Res, 34, 1552-1563.  
16960376 K.Kaneda, K.Ohishi, J.Sekiguchi, and T.Shida (2006).
Characterization of the AP endonucleases from Thermoplasma volcanium and Lactobacillus plantarum: Contributions of two important tryptophan residues to AP site recognition.
  Biosci Biotechnol Biochem, 70, 2213-2221.  
16452411 M.L.Hornback, and R.M.Roop (2006).
The Brucella abortus xthA-1 gene product participates in base excision repair and resistance to oxidative killing but is not required for wild-type virulence in the mouse model.
  J Bacteriol, 188, 1295-1300.  
16434747 T.Yamada, J.Komoto, K.Saiki, K.Konishi, and F.Takusagawa (2006).
Variation of loop sequence alters stability of cytolethal distending toxin (CDT): crystal structure of CDT from Actinobacillus actinomycetemcomitans.
  Protein Sci, 15, 362-372.
PDB code: 2f2f
16093240 A.E.Openshaw, P.R.Race, H.J.Monzó, J.A.Vázquez-Boland, and M.J.Banfield (2005).
Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.
  J Biol Chem, 280, 35011-35017.
PDB code: 1zwx
15637157 A.Weichsel, E.M.Maes, J.F.Andersen, J.G.Valenzuela, T.K.h.Shokhireva, F.A.Walker, and W.R.Montfort (2005).
Heme-assisted S-nitrosation of a proximal thiolate in a nitric oxide transport protein.
  Proc Natl Acad Sci U S A, 102, 594-599.
PDB codes: 1ntf 1y21
16046407 H.Zhu, L.K.Wang, and S.Shuman (2005).
Essential constituents of the 3'-phosphoesterase domain of bacterial DNA ligase D, a nonhomologous end-joining enzyme.
  J Biol Chem, 280, 33707-33715.  
16113242 S.Madhusudan, F.Smart, P.Shrimpton, J.L.Parsons, L.Gardiner, S.Houlbrook, D.C.Talbot, T.Hammonds, P.A.Freemont, M.J.Sternberg, G.L.Dianov, and I.D.Hickson (2005).
Isolation of a small molecule inhibitor of DNA base excision repair.
  Nucleic Acids Res, 33, 4711-4724.  
16165328 ┼.ü.Knizewski, and K.Ginalski (2005).
Bacillus subtilis YkuK protein is distantly related to RNase H.
  FEMS Microbiol Lett, 251, 341-346.  
14982961 B.Ren, J.M.Zhou, and M.Komiyama (2004).
Straightforward detection of SNPs in double-stranded DNA by using exonuclease III/nuclease S1/PNA system.
  Nucleic Acids Res, 32, e42.  
15459284 N.G.Beloglazova, O.O.Kirpota, K.V.Starostin, A.A.Ishchenko, V.I.Yamkovoy, D.O.Zharkov, K.T.Douglas, and G.A.Nevinsky (2004).
Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta.
  Nucleic Acids Res, 32, 5134-5146.  
15247245 N.Maita, T.Anzai, H.Aoyagi, H.Mizuno, and H.Fujiwara (2004).
Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1.
  J Biol Chem, 279, 41067-41076.
PDB code: 1wdu
12829271 D.G.Kehres, and M.E.Maguire (2003).
Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria.
  FEMS Microbiol Rev, 27, 263-290.  
12833551 D.Kumaran, S.Eswaramoorthy, S.E.Gerchman, H.Kycia, F.W.Studier, and S.Swaminathan (2003).
Crystal structure of a putative CN hydrolase from yeast.
  Proteins, 52, 283-291.
PDB code: 1f89
14602897 E.A.Worthey, A.Schnaufer, I.S.Mian, K.Stuart, and R.Salavati (2003).
Comparative analysis of editosome proteins in trypanosomatids.
  Nucleic Acids Res, 31, 6392-6408.  
14585934 E.H.Postel, and B.M.Abramczyk (2003).
Escherichia coli nucleoside diphosphate kinase is a uracil-processing DNA repair nuclease.
  Proc Natl Acad Sci U S A, 100, 13247-13252.  
12573214 J.E.Baggs, and C.B.Green (2003).
Nocturnin, a deadenylase in Xenopus laevis retina: a mechanism for posttranscriptional control of circadian-related mRNA.
  Curr Biol, 13, 189-198.  
12524450 L.Tian, J.M.Sayer, H.Kroth, G.Kalena, D.M.Jerina, and S.Shuman (2003).
Benzo[a]pyrene-dG adduct interference illuminates the interface of vaccinia topoisomerase with the DNA minor groove.
  J Biol Chem, 278, 9905-9911.  
12694197 M.Miertzschke, and T.Greiner-Stöffele (2003).
The xthA gene product of Archaeoglobus fulgidus is an unspecific DNase.
  Eur J Biochem, 270, 1838-1849.  
12641455 Z.A.Doddridge, R.D.Bertram, C.J.Hayes, and P.Soultanas (2003).
Effects of vinylphosphonate internucleotide linkages on the cleavage specificity of exonuclease III and on the activity of DNA polymerase I.
  Biochemistry, 42, 3239-3246.  
12465033 A.Krakowiak, A.Owczarek, M.Koziołkiewicz, and W.J.Stec (2002).
Stereochemical course of Escherichia coli RNase H.
  Chembiochem, 3, 1242-1250.  
11972066 A.Yamagata, Y.Kakuta, R.Masui, and K.Fukuyama (2002).
The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.
  Proc Natl Acad Sci U S A, 99, 5908-5912.
PDB code: 1ir6
11988770 I.V.Shevelev, and U.Hübscher (2002).
The 3' 5' exonucleases.
  Nat Rev Mol Cell Biol, 3, 364-376.  
11889047 J.Chen, Y.C.Chiang, and C.L.Denis (2002).
CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase.
  EMBO J, 21, 1414-1426.  
11960995 M.A.Pope, S.L.Porello, and S.S.David (2002).
Escherichia coli apurinic-apyrimidinic endonucleases enhance the turnover of the adenine glycosylase MutY with G:A substrates.
  J Biol Chem, 277, 22605-22615.  
  11747467 A.Dupressoir, A.P.Morel, W.Barbot, M.P.Loireau, L.Corbo, and T.Heidmann (2001).
Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding.
  BMC Genomics, 2, 9.  
11170417 E.L.Rachofsky, E.Seibert, J.T.Stivers, R.Osman, and J.B.Ross (2001).
Conformation and dynamics of abasic sites in DNA investigated by time-resolved fluorescence of 2-aminopurine.
  Biochemistry, 40, 957-967.  
11700292 E.M.Ostertag, and H.H.Kazazian (2001).
Biology of mammalian L1 retrotransposons.
  Annu Rev Genet, 35, 501-538.  
11160897 H.Yang, W.M.Clendenin, D.Wong, B.Demple, M.M.Slupska, J.H.Chiang, and J.H.Miller (2001).
Enhanced activity of adenine-DNA glycosylase (Myh) by apurinic/apyrimidinic endonuclease (Ape1) in mammalian base excision repair of an A/GO mismatch.
  Nucleic Acids Res, 29, 743-752.  
11238902 I.Unk, L.Haracska, S.Prakash, and L.Prakash (2001).
3'-phosphodiesterase and 3'-->5' exonuclease activities of yeast Apn2 protein and requirement of these activities for repair of oxidative DNA damage.
  Mol Cell Biol, 21, 1656-1661.  
11160881 M.E.Shea, and H.Hiasa (2001).
Replicative helicases can translocate through abasic site-induced covalent topoisomerase IV-DNA complexes.
  Nucleic Acids Res, 29, 614-621.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11348594 Y.Tsujishita, S.Guo, L.E.Stolz, J.D.York, and J.H.Hurley (2001).
Specificity determinants in phosphoinositide dephosphorylation: crystal structure of an archetypal inositol polyphosphate 5-phosphatase.
  Cell, 105, 379-389.
PDB codes: 1i9y 1i9z
10871340 D.G.Rothwell, B.Hang, M.A.Gorman, P.S.Freemont, B.Singer, and I.D.Hickson (2000).
Substitution of Asp-210 in HAP1 (APE/Ref-1) eliminates endonuclease activity but stabilises substrate binding.
  Nucleic Acids Res, 28, 2207-2213.  
10944393 H.Ponstingl, K.Henrick, and J.M.Thornton (2000).
Discriminating between homodimeric and monomeric proteins in the crystalline state.
  Proteins, 41, 47-57.  
10823942 K.Hofmann, S.Tomiuk, G.Wolff, and W.Stoffel (2000).
Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase.
  Proc Natl Acad Sci U S A, 97, 5895-5900.  
10838565 M.Dlaki─ç (2000).
Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases.
  Trends Biochem Sci, 25, 272-273.  
10648607 S.Christensen, G.Pont-Kingdon, and D.Carroll (2000).
Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L.
  Mol Cell Biol, 20, 1219-1226.  
10410797 C.D.Mol, S.S.Parikh, C.D.Putnam, T.P.Lo, and J.A.Tainer (1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
  Annu Rev Biophys Biomol Struct, 28, 101-128.  
10458614 D.J.Hosfield, Y.Guan, B.J.Haas, R.P.Cunningham, and J.A.Tainer (1999).
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
  Cell, 98, 397-408.
PDB codes: 1qtw 1qum
  10022902 F.Janus, N.Albrechtsen, U.Knippschild, L.Wiesmüller, F.Grosse, and W.Deppert (1999).
Different regulation of the p53 core domain activities 3'-to-5' exonuclease and sequence-specific DNA binding.
  Mol Cell Biol, 19, 2155-2168.  
10213597 J.A.Lucas, Y.Masuda, R.A.Bennett, N.S.Strauss, and P.R.Strauss (1999).
Single-turnover analysis of mutant human apurinic/apyrimidinic endonuclease.
  Biochemistry, 38, 4958-4964.  
10898853 J.Lhomme, J.F.Constant, and M.Demeunynck (1999).
Abasic DNA structure, reactivity, and recognition.
  Biopolymers, 52, 65-83.  
9893991 J.T.Stivers, K.W.Pankiewicz, and K.A.Watanabe (1999).
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.
  Biochemistry, 38, 952-963.  
10585943 L.Ayadi, C.Coulombeau, and R.Lavery (1999).
Abasic sites in duplex DNA: molecular modeling of sequence-dependent effects on conformation.
  Biophys J, 77, 3218-3226.  
10546548 L.F.Agnez-Lima, P.Di Mascio, R.L.Napolitano, R.P.Fuchs, and C.F.Menck (1999).
Mutation spectrum induced by singlet oxygen in Escherichia coli deficient in exonuclease III.
  Photochem Photobiol, 70, 505-511.  
  10022867 R.A.Bennett (1999).
The Saccharomyces cerevisiae ETH1 gene, an inducible homolog of exonuclease III that provides resistance to DNA-damaging agents and limits spontaneous mutagenesis.
  Mol Cell Biol, 19, 1800-1809.  
10194301 S.J.Evans, E.J.Shipstone, W.N.Maughan, and B.A.Connolly (1999).
Site-directed mutagenesis of phosphate-contacting amino acids of bovine pancreatic deoxyribonuclease I.
  Biochemistry, 38, 3902-3909.  
10047578 S.S.Parikh, C.D.Mol, D.J.Hosfield, and J.A.Tainer (1999).
Envisioning the molecular choreography of DNA base excision repair.
  Curr Opin Struct Biol, 9, 37-47.  
10540738 T.Shida, T.Ogawa, N.Ogasawara, and J.Sekiguchi (1999).
Characterization of Bacillus subtilis ExoA protein: a multifunctional DNA-repair enzyme similar to the Escherichia coli exonuclease III.
  Biosci Biotechnol Biochem, 63, 1528-1534.  
10090748 X.Yang, P.Tellier, J.Y.Masson, T.Vu, and D.Ramotar (1999).
Characterization of amino acid substitutions that severely alter the DNA repair functions of Escherichia coli endonuclease IV.
  Biochemistry, 38, 3615-3623.  
9761816 A.Carfi, E.Duée, R.Paul-Soto, M.Galleni, J.M.Frère, and O.Dideberg (1998).
X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.
  Acta Crystallogr D Biol Crystallogr, 54, 45-57.
PDB codes: 1bmi 2bmi
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9852053 B.J.Reardon, C.R.Lombardo, and M.Sander (1998).
Drosophila Rrp1 domain structure as defined by limited proteolysis and biophysical analyses.
  J Biol Chem, 273, 33991-33999.  
9922177 G.J.Cost, and J.D.Boeke (1998).
Targeting of human retrotransposon integration is directed by the specificity of the L1 endonuclease for regions of unusual DNA structure.
  Biochemistry, 37, 18081-18093.  
9590283 H.H.Kazazian, and J.V.Moran (1998).
The impact of L1 retrotransposons on the human genome.
  Nat Genet, 19, 19-24.  
9690999 H.H.Kazazian (1998).
Mobile elements and disease.
  Curr Opin Genet Dev, 8, 343-350.  
9852071 J.L.Keck, E.R.Goedken, and S.Marqusee (1998).
Activation/attenuation model for RNase H. A one-metal mechanism with second-metal inhibition.
  J Biol Chem, 273, 34128-34133.  
9592167 J.P.Erzberger, D.Barsky, O.D.Schärer, M.E.Colvin, and D.M.Wilson (1998).
Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases.
  Nucleic Acids Res, 26, 2771-2778.  
9699635 K.Y.Hwang, K.Baek, H.Y.Kim, and Y.Cho (1998).
The crystal structure of flap endonuclease-1 from Methanococcus jannaschii.
  Nat Struct Biol, 5, 707-713.
PDB codes: 1a76 1a77
9603956 P.R.Strauss, and C.M.Holt (1998).
Domain mapping of human apurinic/apyrimidinic endonuclease. Structural and functional evidence for a disordered amino terminus and a tight globular carboxyl domain.
  J Biol Chem, 273, 14435-14441.  
9482842 Q.Feng, G.Schumann, and J.D.Boeke (1998).
Retrotransposon R1Bm endonuclease cleaves the target sequence.
  Proc Natl Acad Sci U S A, 95, 2083-2088.  
  9765213 R.E.Johnson, C.A.Torres-Ramos, T.Izumi, S.Mitra, S.Prakash, and L.Prakash (1998).
Identification of APN2, the Saccharomyces cerevisiae homolog of the major human AP endonuclease HAP1, and its role in the repair of abasic sites.
  Genes Dev, 12, 3137-3143.  
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9843516 S.Cal, K.L.Tan, A.McGregor, and B.A.Connolly (1998).
Conversion of bovine pancreatic DNase I to a repair endonuclease with a high selectivity for abasic sites.
  EMBO J, 17, 7128-7138.  
9520418 S.Tomiuk, K.Hofmann, M.Nix, M.Zumbansen, and W.Stoffel (1998).
Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling?
  Proc Natl Acad Sci U S A, 95, 3638-3643.  
9699633 T.E.Barrett, R.Savva, T.Barlow, T.Brown, J.Jiricny, and L.H.Pearl (1998).
Structure of a DNA base-excision product resembling a cisplatin inter-strand adduct.
  Nat Struct Biol, 5, 697-701.
PDB code: 1mtl
9808040 Y.C.Yuan, R.H.Whitson, Q.Liu, K.Itakura, and Y.Chen (1998).
A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
  Nat Struct Biol, 5, 959-964.
PDB code: 1bmy
9804798 Y.Masuda, R.A.Bennett, and B.Demple (1998).
Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product.
  J Biol Chem, 273, 30352-30359.  
9804799 Y.Masuda, R.A.Bennett, and B.Demple (1998).
Rapid dissociation of human apurinic endonuclease (Ape1) from incised DNA induced by magnesium.
  J Biol Chem, 273, 30360-30365.  
9057832 C.B.Black, and J.A.Cowan (1997).
Inert chromium and cobalt complexes as probes of magnesium-dependent enzymes. Evaluation of the mechanistic role of the essential metal cofactor in Escherichia coli exonuclease III.
  Eur J Biochem, 243, 684-689.  
9032058 D.G.Vassylyev, and K.Morikawa (1997).
DNA-repair enzymes.
  Curr Opin Struct Biol, 7, 103-109.  
9023101 D.M.Wilson, M.Takeshita, and B.Demple (1997).
Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites.
  Nucleic Acids Res, 25, 933-939.  
9782777 D.Suck (1997).
DNA recognition by structure-selective nucleases.
  Biopolymers, 44, 405-421.  
9171104 D.Suh, D.M.Wilson, and L.F.Povirk (1997).
3'-phosphodiesterase activity of human apurinic/apyrimidinic endonuclease at DNA double-strand break ends.
  Nucleic Acids Res, 25, 2495-2500.  
9351835 M.A.Gorman, S.Morera, D.G.Rothwell, E.de La Fortelle, C.D.Mol, J.A.Tainer, I.D.Hickson, and P.S.Freemont (1997).
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites.
  EMBO J, 16, 6548-6558.
PDB code: 1bix
9312137 M.Olivares, C.Alonso, and M.C.López (1997).
The open reading frame 1 of the L1Tc retrotransposon of Trypanosoma cruzi codes for a protein with apurinic-apyrimidinic nuclease activity.
  J Biol Chem, 272, 25224-25228.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
9395327 Y.M.Hsiao, H.C.Ho, W.Y.Wang, M.F.Tam, and T.H.Liao (1997).
Purification and characterization of tilapia (Oreochromis mossambicus) deoxyribonuclease I--primary structure and cDNA sequence.
  Eur J Biochem, 249, 786-791.  
8987998 A.A.Purmal, S.S.Wallace, and Y.W.Kow (1996).
The phosphodiester bond 3' to a deoxyuridine residue is crucial for substrate binding for uracil DNA N-glycosylase.
  Biochemistry, 35, 16630-16637.  
  9003755 A.K.Das, N.R.Helps, P.T.Cohen, and D.Barford (1996).
Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution.
  EMBO J, 15, 6798-6809.
PDB code: 1a6q
8943004 B.Hang, A.Chenna, H.Fraenkel-Conrat, and B.Singer (1996).
An unusual mechanism for the major human apurinic/apyrimidinic (AP) endonuclease involving 5' cleavage of DNA containing a benzene-derived exocyclic adduct in the absence of an AP site.
  Proc Natl Acad Sci U S A, 93, 13737-13741.  
8994877 B.L.Stoddard, and K.E.Flick (1996).
Calcineurin-immunosuppressor complexes.
  Curr Opin Struct Biol, 6, 770-775.  
8932375 D.G.Rothwell, and I.D.Hickson (1996).
Asparagine 212 is essential for abasic site recognition by the human DNA repair endonuclease HAP1.
  Nucleic Acids Res, 24, 4217-4221.  
8650230 F.C.Christians, and L.A.Loeb (1996).
Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.
  Proc Natl Acad Sci U S A, 93, 6124-6128.  
8772379 F.Martín, M.Olivares, M.C.López, and C.Alonso (1996).
Do non-long terminal repeat retrotransposons have nuclease activity?
  Trends Biochem Sci, 21, 283-285.  
  8763868 G.Barzilay, L.J.Walker, D.G.Rothwell, and I.D.Hickson (1996).
Role of the HAP1 protein in repair of oxidative DNA damage and regulation of transcription factors.
  Br J Cancer Suppl, 27, S145-S150.  
8918793 M.Sander, and D.Benhaim (1996).
Drosophila Rrp1 3'-exonuclease: demonstration of DNA sequence dependence and DNA strand specificity.
  Nucleic Acids Res, 24, 3926-3933.  
8805566 N.O.Concha, B.A.Rasmussen, K.Bush, and O.Herzberg (1996).
Crystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis.
  Structure, 4, 823-836.
PDB code: 1znb
8758988 P.Friedhoff, B.Kolmes, O.Gimadutdinow, W.Wende, K.L.Krause, and A.Pingoud (1996).
Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis.
  Nucleic Acids Res, 24, 2632-2639.  
8945517 Q.Feng, J.V.Moran, H.H.Kazazian, and J.D.Boeke (1996).
Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition.
  Cell, 87, 905-916.  
8755524 R.A.Garcia, C.J.Bustamante, and N.O.Reich (1996).
Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
  Proc Natl Acad Sci U S A, 93, 7618-7622.  
8948651 T.Shida, M.Noda, and J.Sekiguchi (1996).
Cleavage of single- and double-stranded DNAs containing an abasic residue by Escherichia coli exonuclease III (AP endonuclease VI).
  Nucleic Acids Res, 24, 4572-4576.  
  7588620 A.Carfi, S.Pares, E.Duée, M.Galleni, C.Duez, J.M.Frère, and O.Dideberg (1995).
The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.
  EMBO J, 14, 4914-4921.
PDB code: 1bmc
  7608140 A.Sancar (1995).
Excision repair in mammalian cells.
  J Biol Chem, 270, 15915-15918.  
7552704 C.Venclovas, and V.Siksnys (1995).
Different enzymes with similar structures involved in Mg(2+)-mediated polynucleotidyl transfer.
  Nat Struct Biol, 2, 838-841.  
7608159 D.M.Wilson, M.Takeshita, A.P.Grollman, and B.Demple (1995).
Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA.
  J Biol Chem, 270, 16002-16007.  
7649997 E.Kanaya, and S.Kanaya (1995).
Reconstitution of Escherichia coli RNase HI from the N-fragment with high helicity and the C-fragment with a disordered structure.
  J Biol Chem, 270, 19853-19860.  
8533150 E.Seeberg, L.Eide, and M.Bjørås (1995).
The base excision repair pathway.
  Trends Biochem Sci, 20, 391-397.  
7664124 G.Barzilay, C.D.Mol, C.N.Robson, L.J.Walker, R.P.Cunningham, J.A.Tainer, and I.D.Hickson (1995).
Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1.
  Nat Struct Biol, 2, 561-568.  
7784208 G.Barzilay, L.J.Walker, C.N.Robson, and I.D.Hickson (1995).
Site-directed mutagenesis of the human DNA repair enzyme HAP1: identification of residues important for AP endonuclease and RNase H activity.
  Nucleic Acids Res, 23, 1544-1550.  
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
7606789 R.J.Roberts (1995).
On base flipping.
  Cell, 82, 9.  
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 codes are shown on the right.