PDBsum entry 1vas

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protein dna_rna links
Hydrolase/DNA PDB id
Protein chain
137 a.a. *
Waters ×143
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Atomic model of a pyrimidine dimer specific excision repair complexed with a DNA substrate: structural basis for damage recognition
Structure: DNA (5'-d( Ap Tp Cp Gp Cp Gp Tp Tp Gp Cp Gp Cp T) chain: b. Engineered: yes. DNA (5'-d( Tp Ap Gp Cp Gp Cp Ap Ap Cp Gp Cp Gp A) chain: c. Engineered: yes. Protein (t4 endonuclease v . Chain: a. Engineered: yes
Source: Synthetic: yes. Enterobacteria phage t4. Organism_taxid: 10665. Gene: denv. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Not given
2.75Å     R-factor:   0.152     R-free:   0.240
Authors: D.G.Vassylyev,T.Kashiwagi,Y.Mikami,M.Ariyoshi,S.Iwai,E.Ohtsu K.Morikawa
Key ref:
D.G.Vassylyev et al. (1995). Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell, 83, 773-782. PubMed id: 8521494 DOI: 10.1016/0092-8674(95)90190-6
08-Sep-95     Release date:   31-Jan-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P04418  (END5_BPT4) -  Endonuclease V
138 a.a.
137 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Deoxyribonuclease (pyrimidine dimer).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage near pyrimidine dimers to products with 5'-phosphate.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     5 terms  


DOI no: 10.1016/0092-8674(95)90190-6 Cell 83:773-782 (1995)
PubMed id: 8521494  
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsuka, K.Morikawa.
T4 endonuclease V is a DNA repair enzyme from bacteriophage T4 that catalyzes the first reaction step of the pyrimidine dimer-specific base excision repair pathway. The crystal structure of this enzyme complexed with a duplex DNA substrate, containing a thymine dimer, has been determined at 2.75 A resolution. The atomic structure of the complex reveals the unique conformation of the DNA duplex, which exhibits a sharp kink with a 60 degree inclination at the central thymine dimer. The adenine base complementary to the 5' side of the thymine dimer is completely flipped out of the DNA duplex and trapped in a cavity on the protein surface. These structural features allow an understanding of the catalytic mechanism and implicate a general mechanism of how other repair enzymes recognize damaged DNA duplexes.
  Selected figure(s)  
Figure 1.
Figure 1. Structue of T4 ndo V-DNA Complex
Figure 3.
igure 3. Protein-DNA nteractions in the Vicinity of the PD
  The above figures are reprinted by permission from Cell Press: Cell (1995, 83, 773-782) copyright 1995.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20577208 C.Biertümpfel, Y.Zhao, Y.Kondo, S.Ramón-Maiques, M.Gregory, J.Y.Lee, C.Masutani, A.R.Lehmann, F.Hanaoka, and W.Yang (2010).
Structure and mechanism of human DNA polymerase eta.
  Nature, 465, 1044-1048.
PDB codes: 3mr2 3mr3 3mr4 3mr5 3mr6 3si8
20156993 R.E.Langlois, and H.Lu (2010).
Boosting the prediction and understanding of DNA-binding domains from sequence.
  Nucleic Acids Res, 38, 3149-3158.  
19465399 D.Kim, S.Reddy, D.Y.Kim, A.Rich, S.Lee, K.K.Kim, and Y.G.Kim (2009).
Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.
  Nucleic Acids Res, 37, 4353-4359.  
19757831 H.A.Dahlmann, V.G.Vaidyanathan, and S.J.Sturla (2009).
Investigating the biochemical impact of DNA damage with structure-based probes: abasic sites, photodimers, alkylation adducts, and oxidative lesions.
  Biochemistry, 48, 9347-9359.  
18704949 S.Biswas, M.Guharoy, and P.Chakrabarti (2009).
Dissection, residue conservation, and structural classification of protein-DNA interfaces.
  Proteins, 74, 643-654.  
19258314 S.Couvé, G.Macé-Aimé, F.Rosselli, and M.K.Saparbaev (2009).
The Human Oxidative DNA Glycosylase NEIL1 Excises Psoralen-induced Interstrand DNA Cross-links in a Three-stranded DNA Structure.
  J Biol Chem, 284, 11963-11970.  
19109889 G.Chu, and W.Yang (2008).
Here comes the sun: recognition of UV-damaged DNA.
  Cell, 135, 1172-1174.  
18086248 K.Yang, and R.J.Stanley (2008).
The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study.
  Photochem Photobiol, 84, 741-749.  
18219418 L.L.O'Neil, and O.Wiest (2008).
Sequence dependence in base flipping: experimental and computational studies.
  Org Biomol Chem, 6, 485-492.  
19074258 R.Pokorny, T.Klar, U.Hennecke, T.Carell, A.Batschauer, and L.O.Essen (2008).
Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome.
  Proc Natl Acad Sci U S A, 105, 21023-21027.
PDB code: 2vtb
18157156 W.Yang (2008).
Structure and mechanism for DNA lesion recognition.
  Cell Res, 18, 184-197.  
17581590 D.G.Vassylyev, M.N.Vassylyeva, A.Perederina, T.H.Tahirov, and I.Artsimovitch (2007).
Structural basis for transcription elongation by bacterial RNA polymerase.
  Nature, 448, 157-162.
PDB code: 2o5i
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
17264133 R.J.Davies, J.F.Malone, Y.Gan, C.J.Cardin, M.P.Lee, and S.Neidle (2007).
High-resolution crystal structure of the intramolecular d(TpA) thymine-adenine photoadduct and its mechanistic implications.
  Nucleic Acids Res, 35, 1048-1053.  
17715144 S.Couvé-Privat, G.Macé, F.Rosselli, and M.K.Saparbaev (2007).
Psoralen-induced DNA adducts are substrates for the base excision repair pathway in human cells.
  Nucleic Acids Res, 35, 5672-5682.  
16282327 E.Malta, G.F.Moolenaar, and N.Goosen (2006).
Base flipping in nucleotide excision repair.
  J Biol Chem, 281, 2184-2194.  
16537484 J.T.Reardon, and A.Sancar (2006).
Repair of DNA-polypeptide crosslinks by human excision nuclease.
  Proc Natl Acad Sci U S A, 103, 4056-4061.  
17115714 R.K.Walker, A.K.McCullough, and R.S.Lloyd (2006).
Uncoupling of nucleotide flipping and DNA bending by the t4 pyrimidine dimer DNA glycosylase.
  Biochemistry, 45, 14192-14200.  
16768442 T.Christian, C.Evilia, and Y.M.Hou (2006).
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline.
  Biochemistry, 45, 7463-7473.  
16547199 Y.Doi, A.Katafuchi, Y.Fujiwara, K.Hitomi, J.A.Tainer, H.Ide, and S.Iwai (2006).
Synthesis and characterization of oligonucleotides containing 2'-fluorinated thymidine glycol as inhibitors of the endonuclease III reaction.
  Nucleic Acids Res, 34, 1540-1551.  
16237447 S.C.Ha, K.Lowenhaupt, A.Rich, Y.G.Kim, and K.K.Kim (2005).
Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.
  Nature, 437, 1183-1186.
PDB code: 2acj
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.  
15576622 A.Mees, T.Klar, P.Gnau, U.Hennecke, A.P.Eker, T.Carell, and L.O.Essen (2004).
Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.
  Science, 306, 1789-1793.
PDB code: 1tez
15121904 J.H.Lee, C.J.Park, J.S.Shin, T.Ikegami, H.Akutsu, and B.S.Choi (2004).
NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.
  Nucleic Acids Res, 32, 2474-2481.
PDB codes: 1pib 1snh
15020710 K.Takasawa, C.Masutani, F.Hanaoka, and S.Iwai (2004).
Chemical synthesis and translesion replication of a cis-syn cyclobutane thymine-uracil dimer.
  Nucleic Acids Res, 32, 1738-1745.  
15472947 L.M.Kundu, U.Linne, M.Marahiel, and T.Carell (2004).
RNA is more UV resistant than DNA: the formation of UV-induced DNA lesions is strongly sequence and conformation dependent.
  Chemistry, 10, 5697-5705.  
14610082 M.G.Meador, L.Rajagopalan, R.S.Lloyd, and M.L.Dodson (2004).
Role of His-16 in turnover of T4 pyrimidine dimer glycosylase.
  J Biol Chem, 279, 3348-3353.  
15326180 R.C.Manuel, K.Hitomi, A.S.Arvai, P.G.House, A.J.Kurtz, M.L.Dodson, A.K.McCullough, J.A.Tainer, and R.S.Lloyd (2004).
Reaction intermediates in the catalytic mechanism of Escherichia coli MutY DNA glycosylase.
  J Biol Chem, 279, 46930-46939.
PDB codes: 1wef 1weg 1wei
15169780 T.Torizawa, T.Ueda, S.Kuramitsu, K.Hitomi, T.Todo, S.Iwai, K.Morikawa, and I.Shimada (2004).
Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses.
  J Biol Chem, 279, 32950-32956.  
14661275 A.David, N.Bleimling, C.Beuck, J.M.Lehn, E.Weinhold, and M.P.Teulade-Fichou (2003).
DNA mismatch-specific base flipping by a bisacridine macrocycle.
  Chembiochem, 4, 1326-1331.  
12945584 B.Durbeej, and L.A.Eriksson (2003).
On the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: why are thymines more reactive?
  Photochem Photobiol, 78, 159-167.  
12626685 E.S.Miller, E.Kutter, G.Mosig, F.Arisaka, T.Kunisawa, and W.Rüger (2003).
Bacteriophage T4 genome.
  Microbiol Mol Biol Rev, 67, 86.  
12783877 H.C.Ahn, T.Ohkubo, S.Iwai, K.Morikawa, and B.J.Lee (2003).
Interaction of T4 endonuclease V with DNA: importance of the flexible loop regions in protein-DNA interaction.
  J Biol Chem, 278, 30985-30992.  
12904819 H.Ling, F.Boudsocq, B.S.Plosky, R.Woodgate, and W.Yang (2003).
Replication of a cis-syn thymine dimer at atomic resolution.
  Nature, 424, 1083-1087.
PDB codes: 1pm0 1pm8 1ryr 1rys
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
12456887 H.Park, K.Zhang, Y.Ren, S.Nadji, N.Sinha, J.S.Taylor, and C.Kang (2002).
Crystal structure of a DNA decamer containing a cis-syn thymine dimer.
  Proc Natl Acad Sci U S A, 99, 15965-15970.
PDB codes: 1mv7 1n4e 1sm5 1t4i
11842222 I.G.Minko, Y.Zou, and R.S.Lloyd (2002).
Incision of DNA-protein crosslinks by UvrABC nuclease suggests a potential repair pathway involving nucleotide excision repair.
  Proc Natl Acad Sci U S A, 99, 1905-1909.  
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 code: 1kfv
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.  
11423420 M.Feig, M.Zacharias, and B.M.Pettitt (2001).
Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.
  Biophys J, 81, 352-370.  
11223884 O.D.Schärer, and J.Jiricny (2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
  Bioessays, 23, 270-281.  
11812824 T.Mizukoshi, T.S.Kodama, Y.Fujiwara, T.Furuno, M.Nakanishi, and S.Iwai (2001).
Structural study of DNA duplexes containing the (6-4) photoproduct by fluorescence resonance energy transfer.
  Nucleic Acids Res, 29, 4948-4954.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11106395 A.Y.Lau, M.D.Wyatt, B.J.Glassner, L.D.Samson, and T.Ellenberger (2000).
Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.
  Proc Natl Acad Sci U S A, 97, 13573-13578.
PDB codes: 1ewn 1f4r 1f6o
10734199 J.H.Lee, Y.J.Choi, and B.S.Choi (2000).
Solution structure of the DNA decamer duplex containing a 3'-T x T basepair of the cis-syn cyclobutane pyrimidine dimer: implication for the mutagenic property of the cis-syn dimer.
  Nucleic Acids Res, 28, 1794-1801.
PDB code: 1ql5
10921868 M.Sugahara, T.Mikawa, T.Kumasaka, M.Yamamoto, R.Kato, K.Fukuyama, Y.Inoue, and S.Kuramitsu (2000).
Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
  EMBO J, 19, 3857-3869.
PDB code: 1ee8
10816003 R.Osman, M.Fuxreiter, and N.Luo (2000).
Specificity of damage recognition and catalysis of DNA repair.
  Comput Chem, 24, 331-339.  
10675345 T.Hollis, Y.Ichikawa, and T.Ellenberger (2000).
DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.
  EMBO J, 19, 758-766.
PDB code: 1diz
10872450 A.K.McCullough, M.L.Dodson, and R.S.Lloyd (1999).
Initiation of base excision repair: glycosylase mechanisms and structures.
  Annu Rev Biochem, 68, 255-285.  
10220317 B.W.Allan, N.O.Reich, and J.M.Beechem (1999).
Measurement of the absolute temporal coupling between DNA binding and base flipping.
  Biochemistry, 38, 5308-5314.  
10383435 B.W.Allan, R.Garcia, K.Maegley, J.Mort, D.Wong, W.Lindstrom, J.M.Beechem, and N.O.Reich (1999).
DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.
  J Biol Chem, 274, 19269-19275.  
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.  
10454618 C.L.Chepanoske, S.L.Porello, T.Fujiwara, H.Sugiyama, and S.S.David (1999).
Substrate recognition by Escherichia coli MutY using substrate analogs.
  Nucleic Acids Res, 27, 3197-3204.  
10350454 D.M.Noll, A.Gogos, J.A.Granek, and N.D.Clarke (1999).
The C-terminal domain of the adenine-DNA glycosylase MutY confers specificity for 8-oxoguanine.adenine mispairs and may have evolved from MutT, an 8-oxo-dGTPase.
  Biochemistry, 38, 6374-6379.  
10518532 D.M.van Aalten, D.A.Erlanson, G.L.Verdine, and L.Joshua-Tor (1999).
A structural snapshot of base-pair opening in DNA.
  Proc Natl Acad Sci U S A, 96, 11809-11814.
PDB code: 1cw9
10581233 F.Thoma (1999).
Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair.
  EMBO J, 18, 6585-6598.  
10075917 H.Raaijmakers, O.Vix, I.Törõ, S.Golz, B.Kemper, and D.Suck (1999).
X-ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain-swapped dimer architecture.
  EMBO J, 18, 1447-1458.
PDB code: 1en7
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.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10601012 K.Theis, P.J.Chen, M.Skorvaga, B.Van Houten, and C.Kisker (1999).
Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.
  EMBO J, 18, 6899-6907.
PDB codes: 1d9x 1d9z
10454605 S.Kanno, S.Iwai, M.Takao, and A.Yasui (1999).
Repair of apurinic/apyrimidinic sites by UV damage endonuclease; a repair protein for UV and oxidative damage.
  Nucleic Acids Res, 27, 3096-3103.  
10446184 S.Tornaletti, D.Reines, and P.C.Hanawalt (1999).
Structural characterization of RNA polymerase II complexes arrested by a cyclobutane pyrimidine dimer in the transcribed strand of template DNA.
  J Biol Chem, 274, 24124-24130.  
10581234 T.E.Barrett, O.D.Schärer, R.Savva, T.Brown, J.Jiricny, G.L.Verdine, and L.H.Pearl (1999).
Crystal structure of a thwarted mismatch glycosylase DNA repair complex.
  EMBO J, 18, 6599-6609.
PDB code: 1mwj
10391953 Y.Fujiwara, C.Masutani, T.Mizukoshi, J.Kondo, F.Hanaoka, and S.Iwai (1999).
Characterization of DNA recognition by the human UV-damaged DNA-binding protein.
  J Biol Chem, 274, 20027-20033.  
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.
  Cell, 99, 433-442.
PDB code: 1d8v
9582353 A.K.McCullough, M.T.Romberg, S.Nyaga, Y.Wei, T.G.Wood, J.S.Taylor, J.L.Van Etten, M.L.Dodson, and R.S.Lloyd (1998).
Characterization of a novel cis-syn and trans-syn-II pyrimidine dimer glycosylase/AP lyase from a eukaryotic algal virus, Paramecium bursaria chlorella virus-1.
  J Biol Chem, 273, 13136-13142.  
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.  
9685377 B.J.Vande Berg, and G.B.Sancar (1998).
Evidence for dinucleotide flipping by DNA photolyase.
  J Biol Chem, 273, 20276-20284.  
9442083 B.W.Allan, J.M.Beechem, W.M.Lindstrom, and N.O.Reich (1998).
Direct real time observation of base flipping by the EcoRI DNA methyltransferase.
  J Biol Chem, 273, 2368-2373.  
9751641 D.P.Hornby, and G.C.Ford (1998).
Protein-mediated base flipping.
  Curr Opin Biotechnol, 9, 354-358.  
9642291 E.Nicolas, J.M.Beggs, B.M.Haltiwanger, and T.F.Taraschi (1998).
A new class of DNA glycosylase/apurinic/apyrimidinic lyases that act on specific adenines in single-stranded DNA.
  J Biol Chem, 273, 17216-17220.  
  9632775 F.Coin, P.Frit, B.Viollet, B.Salles, and J.M.Egly (1998).
TATA binding protein discriminates between different lesions on DNA, resulting in a transcription decrease.
  Mol Cell Biol, 18, 3907-3914.  
9417045 G.Panayotou, T.Brown, T.Barlow, L.H.Pearl, and R.Savva (1998).
Direct measurement of the substrate preference of uracil-DNA glycosylase.
  J Biol Chem, 273, 45-50.  
9518486 H.Yamaguchi, D.M.van Aalten, M.Pinak, A.Furukawa, and R.Osman (1998).
Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion.
  Nucleic Acids Res, 26, 1939-1946.  
9535832 O.D.Schärer, H.M.Nash, J.Jiricny, J.Laval, and G.L.Verdine (1998).
Specific binding of a designed pyrrolidine abasic site analog to multiple DNA glycosylases.
  J Biol Chem, 273, 8592-8597.  
9862809 P.H.Tran, Z.R.Korszun, S.Cerritelli, S.S.Springhorn, and S.A.Lacks (1998).
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.
  Structure, 6, 1563-1575.
PDB code: 2dpm
9427764 U.Schieferstein, and F.Thoma (1998).
Site-specific repair of cyclobutane pyrimidine dimers in a positioned nucleosome by photolyase and T4 endonuclease V in vitro.
  EMBO J, 17, 306-316.  
9685504 Y.Jing, J.F.Kao, and J.S.Taylor (1998).
Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT.
  Nucleic Acids Res, 26, 3845-3853.  
9341165 A.K.McCullough, M.L.Dodson, O.D.Schärer, and R.S.Lloyd (1997).
The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
  J Biol Chem, 272, 27210-27217.  
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.  
9493966 G.Lapointe, C.Winchcombe-Forhan, and D.H.Evans (1997).
Genotoxin resistance properties of transgenic tobacco plants expressing bacteriophage T4 DenV and Saccharomyces cerevisiae Apn1 proteins.
  Biochem Cell Biol, 75, 435-443.  
9125491 G.P.Mullen, and S.H.Wilson (1997).
DNA polymerase beta in abasic site repair: a structurally conserved helix-hairpin-helix motif in lesion detection by base excision repair enzymes.
  Biochemistry, 36, 4713-4717.  
9333324 J.L.Schwartz, J.S.Rice, B.A.Luxon, J.M.Sayer, G.Xie, H.J.Yeh, X.Liu, D.M.Jerina, and D.G.Gorenstein (1997).
Solution structure of the minor conformer of a DNA duplex containing a dG mismatch opposite a benzo[a]pyrene diol epoxide/dA adduct: glycosidic rotation from syn to anti at the modified deoxyadenosine.
  Biochemistry, 36, 11069-11076.
PDB code: 1bps
  9371633 J.Sekiguchi, and S.Shuman (1997).
Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
  J Virol, 71, 9679-9684.  
9079656 K.Goodtzova, S.Kanugula, S.Edara, G.T.Pauly, R.C.Moschel, and A.E.Pegg (1997).
Repair of O6-benzylguanine by the Escherichia coli Ada and Ogt and the human O6-alkylguanine-DNA alkyltransferases.
  J Biol Chem, 272, 8332-8339.  
9125531 L.E.Rabow, and Y.W.Kow (1997).
Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis.
  Biochemistry, 36, 5084-5096.  
  9097450 M.Furuta, J.O.Schrader, H.S.Schrader, T.A.Kokjohn, S.Nyaga, A.K.McCullough, R.S.Lloyd, D.E.Burbank, D.Landstein, L.Lane, and J.L.Van Etten (1997).
Chlorella virus PBCV-1 encodes a homolog of the bacteriophage T4 UV damage repair gene denV.
  Appl Environ Microbiol, 63, 1551-1556.  
9060440 M.G.Cooney, and J.H.Miller (1997).
Calculated distortions of duplex DNA by a cis, syn cyclobutane thymine dimer are unaffected by a 3' TpA step.
  Nucleic Acids Res, 25, 1432-1436.  
9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
  J Biol Chem, 272, 17966-17971.  
9667887 O.D.Schärer, L.Deng, and G.L.Verdine (1997).
Chemical approaches toward understanding base excision DNA repair.
  Curr Opin Chem Biol, 1, 526-531.  
9144158 O.D.Schärer, T.Kawate, P.Gallinari, J.Jiricny, and G.L.Verdine (1997).
Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors.
  Proc Natl Acad Sci U S A, 94, 4878-4883.  
9045609 P.J.Dandliker, R.E.Holmlin, and J.K.Barton (1997).
Oxidative thymine dimer repair in the DNA helix.
  Science, 275, 1465-1468.  
9380498 P.Ordoukhanian, and J.S.Taylor (1997).
Solid phase-supported thymine dimers for the construction of dimer-containing DNA by combined chemical and enzymatic synthesis: a potentially general method for the efficient incorporation of modified nucleotides into DNA.
  Nucleic Acids Res, 25, 3783-3786.  
9405373 P.Vichi, F.Coin, J.P.Renaud, W.Vermeulen, J.H.Hoeijmakers, D.Moras, and J.M.Egly (1997).
Cisplatin- and UV-damaged DNA lure the basal transcription factor TFIID/TBP.
  EMBO J, 16, 7444-7456.  
9287157 R.C.Manuel, and R.S.Lloyd (1997).
Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
  Biochemistry, 36, 11140-11152.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
8995288 S.Cal, and B.A.Connolly (1997).
DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides.
  J Biol Chem, 272, 490-496.  
9100001 S.G.Nyaga, M.L.Dodson, and R.S.Lloyd (1997).
Role of specific amino acid residues in T4 endonuclease V that alter nontarget DNA binding.
  Biochemistry, 36, 4080-4088.  
9207024 S.Kumar, J.R.Horton, G.D.Jones, R.T.Walker, R.J.Roberts, and X.Cheng (1997).
DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
  Nucleic Acids Res, 25, 2773-2783.
PDB code: 6mht
9207015 W.Gong, M.O'Gara, R.M.Blumenthal, and X.Cheng (1997).
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
  Nucleic Acids Res, 25, 2702-2715.
PDB code: 1boo
9380513 Y.Komatsu, T.Tsujino, T.Suzuki, O.Nikaido, and E.Ohtsuka (1997).
Antigen structural requirements for recognition by a cyclobutane thymine dimer-specific monoclonal antibody.
  Nucleic Acids Res, 25, 3889-3894.  
8943268 A.K.McCullough, O.Schärer, G.L.Verdine, and R.S.Lloyd (1996).
Structural determinants for specific recognition by T4 endonuclease V.
  J Biol Chem, 271, 32147-32152.  
8942637 B.W.Allan, and N.O.Reich (1996).
Targeted base stacking disruption by the EcoRI DNA methyltransferase.
  Biochemistry, 35, 14757-14762.  
8994964 D.G.Vassylyev, and K.Morikawa (1996).
Precluding uracil from DNA.
  Structure, 4, 1381-1385.  
8783394 H.Nakamura (1996).
Roles of electrostatic interaction in proteins.
  Q Rev Biophys, 29, 1.  
8653795 H.S.Subramanya, A.J.Doherty, S.R.Ashford, and D.B.Wigley (1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
  Cell, 85, 607-615.
PDB code: 1a0i
  8994802 I.Ahmad, and D.N.Rao (1996).
Chemistry and biology of DNA methyltransferases.
  Crit Rev Biochem Mol Biol, 31, 361-380.  
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.  
8805547 X.Cheng, and R.M.Blumenthal (1996).
Finding a basis for flipping bases.
  Structure, 4, 639-645.  
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.