PDBsum entry 1bix

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protein metals links
DNA repair PDB id
Protein chain
275 a.a. *
_SM ×4
Waters ×155
* Residue conservation analysis
PDB id:
Name: DNA repair
Title: The crystal structure of the human DNA repair endonuclease hap1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites
Structure: Ap endonuclease 1. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.20Å     R-factor:   0.184     R-free:   0.269
Authors: M.A.Gorman,S.Morera,D.G.Rothwell,E.De La Fortelle,C.D.Mol, J.A.Tainer,I.D.Hickson,P.S.Freemont
Key ref:
M.A.Gorman et al. (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. PubMed id: 9351835 DOI: 10.1093/emboj/16.21.6548
19-Jun-98     Release date:   22-Jun-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P27695  (APEX1_HUMAN) -  DNA-(apurinic or apyrimidinic site) lyase
318 a.a.
275 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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!
  Cellular component     intracellular   12 terms 
  Biological process     cellular response to cAMP   24 terms 
  Biochemical function     protein binding     27 terms  


DOI no: 10.1093/emboj/16.21.6548 EMBO J 16:6548-6558 (1997)
PubMed id: 9351835  
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites.
M.A.Gorman, S.Morera, D.G.Rothwell, La Fortelle, C.D.Mol, J.A.Tainer, I.D.Hickson, P.S.Freemont.
The structure of the major human apurinic/ apyrimidinic endonuclease (HAP1) has been solved at 2.2 A resolution. The enzyme consists of two symmetrically related domains of similar topology and has significant structural similarity to both bovine DNase I and its Escherichia coli homologue exonuclease III (EXOIII). A structural comparison of these enzymes reveals three loop regions specific to HAP1 and EXOIII. These loop regions apparently act in DNA abasic site (AP) recognition and cleavage since DNase I, which lacks these loops, correspondingly lacks AP site specificity. The HAP1 structure furthermore suggests a mechanism for AP site binding which involves the recognition of the deoxyribose moiety in an extrahelical conformation, rather than a 'flipped-out' base opposite the AP site.
  Selected figure(s)  
Figure 3.
Figure 3 Structural similarity between the overall folds of DNase I, HAP1 and EXOIII. For reference, DNase I is shown complexed to DNA (Lahm and Suck, 1991), and -helices are coloured blue, with -strands in magenta. The yellow arrows indicate the loop regions which are present in HAP1 and EXOIII, but are absent from DNase I (see text).
Figure 8.
Figure 8 Electrostatic surface potential map of HAP1 with modelled DNA. The surface was generated using the program GRASP (Nicholls et al., 1991) with red, blue and white corresponding to negative, positive and neutral charged regions, respectively. The modelled DNA is represented as a stick model coloured gold. The AP site lies directly in the active site cavity.
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 6548-6558) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21353648 D.O.Onyango, A.Naguleswaran, S.Delaplane, A.Reed, M.R.Kelley, M.M.Georgiadis, and W.J.Sullivan (2011).
Base excision repair apurinic/apyrimidinic endonucleases in apicomplexan parasite Toxoplasma gondii.
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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.
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20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
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20808930 A.Gelin, M.Redrejo-Rodríguez, J.Laval, O.S.Fedorova, M.Saparbaev, and A.A.Ishchenko (2010).
Genetic and biochemical characterization of human AP endonuclease 1 mutants deficient in nucleotide incision repair activity.
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19888678 B.A.Manvilla, K.M.Varney, and A.C.Drohat (2010).
Chemical shift assignments for human apurinic/apyrimidinic endonuclease 1.
  Biomol NMR Assign, 4, 5-8.  
20711647 C.S.Busso, M.W.Lake, and T.Izumi (2010).
Posttranslational modification of mammalian AP endonuclease (APE1).
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20699270 D.Fantini, C.Vascotto, D.Marasco, C.D'Ambrosio, M.Romanello, L.Vitagliano, C.Pedone, M.Poletto, L.Cesaratto, F.Quadrifoglio, A.Scaloni, J.P.Radicella, and G.Tell (2010).
Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functions.
  Nucleic Acids Res, 38, 8239-8256.  
20809131 D.M.Wilson, and A.Simeonov (2010).
Small molecule inhibitors of DNA repair nuclease activities of APE1.
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20706766 G.Tell, D.Fantini, and F.Quadrifoglio (2010).
Understanding different functions of mammalian AP endonuclease (APE1) as a promising tool for cancer treatment.
  Cell Mol Life Sci, 67, 3589-3608.  
20446770 J.Shlomai (2010).
Redox control of protein-DNA interactions: from molecular mechanisms to significance in signal transduction, gene expression, and DNA replication.
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19764832 M.Luo, H.He, M.R.Kelley, and M.M.Georgiadis (2010).
Redox regulation of DNA repair: implications for human health and cancer therapeutic development.
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20872611 P.I.Okagbare, and S.A.Soper (2010).
Polymer-based dense fluidic networks for high throughput screening with ultrasensitive fluorescence detection.
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20056333 R.Abbotts, and S.Madhusudan (2010).
Human AP endonuclease 1 (APE1): from mechanistic insights to druggable target in cancer.
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18715143 A.Bapat, M.L.Fishel, and M.R.Kelley (2009).
Going ape as an approach to cancer therapeutics.
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19188445 C.Vascotto, D.Fantini, M.Romanello, L.Cesaratto, M.Deganuto, A.Leonardi, J.P.Radicella, M.R.Kelley, C.D'Ambrosio, A.Scaloni, F.Quadrifoglio, and G.Tell (2009).
APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process.
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18976116 G.Tell, F.Quadrifoglio, C.Tiribelli, and M.R.Kelley (2009).
The many functions of APE1/Ref-1: not only a DNA repair enzyme.
  Antioxid Redox Signal, 11, 601-620.  
  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.
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18715144 K.K.Bhakat, A.K.Mantha, and S.Mitra (2009).
Transcriptional regulatory functions of mammalian AP-endonuclease (APE1/Ref-1), an essential multifunctional protein.
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19123919 S.T.Mundle, J.C.Delaney, J.M.Essigmann, and P.R.Strauss (2009).
Enzymatic mechanism of human apurinic/apyrimidinic endonuclease against a THF AP site model substrate.
  Biochemistry, 48, 19-26.  
19181704 V.M.Castillo-Acosta, L.M.Ruiz-Pérez, W.Yang, D.González-Pacanowska, and A.E.Vidal (2009).
Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family.
  Nucleic Acids Res, 37, 1829-1842.  
18436236 A.K.Mantha, N.Oezguen, K.K.Bhakat, T.Izumi, W.Braun, and S.Mitra (2008).
Unusual role of a cysteine residue in substrate binding and activity of human AP-endonuclease 1.
  J Mol Biol, 379, 28-37.  
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.  
18586825 K.Ando, S.Hirao, Y.Kabe, Y.Ogura, I.Sato, Y.Yamaguchi, T.Wada, and H.Handa (2008).
A new APE1/Ref-1-dependent pathway leading to reduction of NF-kappaB and AP-1, and activation of their DNA-binding activity.
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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.  
18627350 M.Luo, S.Delaplane, A.Jiang, A.Reed, Y.He, M.Fishel, R.L.Nyland, R.F.Borch, X.Qiao, M.M.Georgiadis, and M.R.Kelley (2008).
Role of the multifunctional DNA repair and redox signaling protein Ape1/Ref-1 in cancer and endothelial cells: small-molecule inhibition of the redox function of Ape1.
  Antioxid Redox Signal, 10, 1853-1867.  
18579163 M.M.Georgiadis, M.Luo, R.K.Gaur, S.Delaplane, X.Li, and M.R.Kelley (2008).
Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease.
  Mutat Res, 643, 54-63.
PDB codes: 2o3c 2o3h
18669665 R.H.Porecha, and J.T.Stivers (2008).
Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils.
  Proc Natl Acad Sci U S A, 105, 10791-10796.  
18427783 T.Accetto, and G.Avgustin (2008).
Expression of nuclease gene nucA, a member of an operon putatively involved in uracil removal from DNA and its subsequent reuse in Prevotella bryantii.
  Arch Microbiol, 190, 111-117.  
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.
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PDB codes: 2jc4 2jc5
17403694 J.Qu, G.H.Liu, B.Huang, and C.Chen (2007).
Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of cysteines 93 and 310.
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17560642 M.L.Fishel, and M.R.Kelley (2007).
The DNA base excision repair protein Ape1/Ref-1 as a therapeutic and chemopreventive target.
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17537809 N.Maita, H.Aoyagi, M.Osanai, M.Shirakawa, and H.Fujiwara (2007).
Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies.
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PDB code: 2ei9
17427952 N.Oezguen, C.H.Schein, S.R.Peddi, T.D.Power, T.Izumi, and W.Braun (2007).
A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1.
  Proteins, 68, 313-323.  
17724035 R.L.Maher, and L.B.Bloom (2007).
Pre-steady-state kinetic characterization of the AP endonuclease activity of human AP endonuclease 1.
  J Biol Chem, 282, 30577-30585.  
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
16700550 H.Song, S.Bao, S.Ramanadham, and J.Turk (2006).
Effects of biological oxidants on the catalytic activity and structure of group VIA phospholipase A2.
  Biochemistry, 45, 6392-6406.  
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.  
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
15913400 B.Jakob, J.H.Rudolph, N.Gueven, M.F.Lavin, and G.Taucher-Scholz (2005).
Live cell imaging of heavy-ion-induced radiation responses by beamline microscopy.
  Radiat Res, 163, 681-690.  
15942031 E.B.Jackson, C.A.Theriot, R.Chattopadhyay, S.Mitra, and T.Izumi (2005).
Analysis of nuclear transport signals in the human apurinic/apyrimidinic endonuclease (APE1/Ref1).
  Nucleic Acids Res, 33, 3303-3312.  
15706084 G.Tell, G.Damante, D.Caldwell, and M.R.Kelley (2005).
The intracellular localization of APE1/Ref-1: more than a passive phenomenon?
  Antioxid Redox Signal, 7, 367-384.  
16199668 M.S.Almeida, T.Herrmann, W.Peti, I.A.Wilson, and K.Wüthrich (2005).
NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima: implications for 216 homologous DUF59 proteins.
  Protein Sci, 14, 2880-2886.
PDB codes: 1uwd 1wcj
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.  
15155853 A.B.Guliaev, B.Hang, and B.Singer (2004).
Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C.
  Nucleic Acids Res, 32, 2844-2852.  
15499577 B.Hang (2004).
Repair of exocyclic DNA adducts: rings of complexity.
  Bioessays, 26, 1195-1208.  
  15159209 D.R.McNeill, A.Narayana, H.K.Wong, and D.M.Wilson (2004).
Inhibition of Ape1 nuclease activity by lead, iron, and cadmium.
  Environ Health Perspect, 112, 799-804.  
14704345 L.Gros, A.A.Ishchenko, H.Ide, R.H.Elder, and M.K.Saparbaev (2004).
The major human AP endonuclease (Ape1) is involved in the nucleotide incision repair pathway.
  Nucleic Acids Res, 32, 73-81.  
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
15274918 O.Weichenrieder, K.Repanas, and A.Perrakis (2004).
Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
  Structure, 12, 975-986.
PDB code: 1vyb
12842873 A.Yoshida, Y.Urasaki, M.Waltham, A.C.Bergman, P.Pourquier, D.G.Rothwell, M.Inuzuka, J.N.Weinstein, T.Ueda, E.Appella, I.D.Hickson, and Y.Pommier (2003).
Human apurinic/apyrimidinic endonuclease (Ape1) and its N-terminal truncated form (AN34) are involved in DNA fragmentation during apoptosis.
  J Biol Chem, 278, 37768-37776.  
12622833 C.B.Green (2003).
Molecular control of Xenopus retinal circadian rhythms.
  J Neuroendocrinol, 15, 350-354.  
12552119 C.Nguyen, J.L.Teo, A.Matsuda, M.Eguchi, E.Y.Chi, W.R.Henderson, and M.Kahn (2003).
Chemogenomic identification of Ref-1/AP-1 as a therapeutic target for asthma.
  Proc Natl Acad Sci U S A, 100, 1169-1173.  
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
12857737 D.Wong, M.S.DeMott, and B.Demple (2003).
Modulation of the 3'-->5'-exonuclease activity of human apurinic endonuclease (Ape1) by its 5'-incised Abasic DNA product.
  J Biol Chem, 278, 36242-36249.  
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.  
12624104 K.M.Chou, and Y.C.Cheng (2003).
The exonuclease activity of human apurinic/apyrimidinic endonuclease (APE1). Biochemical properties and inhibition by the natural dinucleotide Gp4G.
  J Biol Chem, 278, 18289-18296.  
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.  
12590136 P.Viswanathan, J.Chen, Y.C.Chiang, and C.L.Denis (2003).
Identification of multiple RNA features that influence CCR4 deadenylation activity.
  J Biol Chem, 278, 14949-14955.  
12445335 C.H.Schein, N.Ozgün, T.Izumi, and W.Braun (2002).
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases.
  BMC Bioinformatics, 3, 37.  
11739700 H.J.Zhang, V.J.Drake, L.Xu, J.Hu, F.E.Domann, L.W.Oberley, and K.C.Kregel (2002).
Redox regulation of adenovirus-induced AP-1 activation by overexpression of manganese-containing superoxide dismutase.
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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.  
11707423 A.E.Vidal, S.Boiteux, I.D.Hickson, and J.P.Radicella (2001).
XRCC1 coordinates the initial and late stages of DNA abasic site repair through protein-protein interactions.
  EMBO J, 20, 6530-6539.  
11317342 A.Ronen, and B.W.Glickman (2001).
Human DNA repair genes.
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11264462 C.J.Norbury, and I.D.Hickson (2001).
Cellular responses to DNA damage.
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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.  
11554453 M.R.Kelley, and S.H.Parsons (2001).
Redox regulation of the DNA repair function of the human AP endonuclease Ape1/ref-1.
  Antioxid Redox Signal, 3, 671-683.  
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.  
11213487 J.Qin, Y.Yang, A.Velyvis, and A.Gronenborn (2000).
Molecular views of redox regulation: three-dimensional structures of redox regulatory proteins and protein complexes.
  Antioxid Redox Signal, 2, 827-840.  
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.Dlakić (2000).
Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases.
  Trends Biochem Sci, 25, 272-273.  
11024165 M.Z.Hadi, M.A.Coleman, K.Fidelis, H.W.Mohrenweiser, and D.M.Wilson (2000).
Functional characterization of Ape1 variants identified in the human population.
  Nucleic Acids Res, 28, 3871-3879.  
10569923 A.Claiborne, J.I.Yeh, T.C.Mallett, J.Luba, E.J.Crane, V.Charrier, and D.Parsonage (1999).
Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation.
  Biochemistry, 38, 15407-15416.  
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.  
10523305 C.Gaiddon, N.C.Moorthy, and C.Prives (1999).
Ref-1 regulates the transactivation and pro-apoptotic functions of p53 in vivo.
  EMBO J, 18, 5609-5621.  
10600117 D.C.Carey, and P.R.Strauss (1999).
Human apurinic/apyrimidinic endonuclease is processive.
  Biochemistry, 38, 16553-16560.  
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
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.  
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.  
  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.  
10583946 T.Lindahl, and R.D.Wood (1999).
Quality control by DNA repair.
  Science, 286, 1897-1905.  
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.  
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.  
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.  
9783745 M.O'Gara, J.R.Horton, R.J.Roberts, and X.Cheng (1998).
Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
  Nat Struct Biol, 5, 872-877.
PDB codes: 7mht 8mht 9mht
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.
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9624147 R.D.Beger, and P.H.Bolton (1998).
Structures of apurinic and apyrimidinic sites in duplex DNAs.
  J Biol Chem, 273, 15565-15573.
PDB codes: 1a9g 1a9h 1a9i 1a9j
  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.  
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.
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9724657 S.S.Parikh, C.D.Mol, G.Slupphaug, S.Bharati, H.E.Krokan, and J.A.Tainer (1998).
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
  EMBO J, 17, 5214-5226.
PDB codes: 1akz 1ssp 2ssp
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
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.
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9782777 D.Suck (1997).
DNA recognition by structure-selective nucleases.
  Biopolymers, 44, 405-421.  
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.