Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor

Manvilla, Brittney A.; Pozharski, Edwin; Toth, Eric A.; Drohat, Alexander C.

doi:10.1107/s0907444913027042

Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg²⁺ cofactor

Journal Article · Tue Nov 19 00:00:00 EST 2013 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/s0907444913027042· OSTI ID:1625685

Manvilla, Brittney A. ^[1]; Pozharski, Edwin ^[2]; Toth, Eric A. ^[3]; Drohat, Alexander C. ^[3]

Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Biochemistry and Molecular Biology; DOE/OSTI
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Pharmaceutical Sciences
Univ. of Maryland Baltimore County (UMBC), Baltimore, MD (United States). School of Medicine. Dept. of Biochemistry and Molecular Biology

Apurinic/apyrimidinic endonuclease 1 (APE1) mediates the repair of abasic sites and other DNA lesions and is essential for base-excision repair and strand-break repair pathways. APE1 hydrolyzes the phosphodiester bond at abasic sites, producing 5'-deoxyribose phosphate and the 3'-OH primer needed for repair synthesis. It also has additional repair activities, including the removal of 3'-blocking groups. APE1 is a powerful enzyme that absolutely requires Mg²⁺, but the stoichiometry and catalytic function of the divalent cation remain unresolved for APE1 and for other enzymes in the DNase I superfamily. Previously reported structures of DNA-free APE1 contained either Sm³⁺ or Pb²⁺ in the active site. However, these are poor surrogates for Mg²⁺ because Sm³⁺is not a cofactor and Pb²⁺ inhibits APE1, and their coordination geometry is expected to differ from that of Mg²⁺. A crystal structure of human APE1 was solved at 1.92 Å resolution with a single Mg²⁺ ion in the active site. The structure reveals ideal octahedral coordination of Mg²⁺ via two carboxylate groups and four water molecules. One residue that coordinates Mg²⁺ directly and two that bind inner-sphere water molecules are strictly conserved in the DNase I superfamily. This structure, together with a recent structure of the enzyme–product complex, inform on the stoichiometry and the role of Mg²⁺ in APE1-catalyzed reactions.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Maryland, College Park, MD (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI ID:: 1625685

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography, Journal Name: Acta Crystallographica. Section D: Biological Crystallography Journal Issue: 12 Vol. 69; ISSN ABCRE6; ISSN 0907-4449

Publisher:: International Union of CrystallographyCopyright Statement

Country of Publication:: United States

Language:: English

References (55)

Lead promotes abasic site accumulation and co-mutagenesis in mammalian cells by inhibiting the major abasic endonuclease Ape1 McNeill, Daniel R.; Wong, Heng-Kuan; Narayana, Avinash Molecular Carcinogenesis, Vol. 46, Issue 2 https://doi.org/10.1002/mc.20196	journal	February 2007
A “moving metal mechanism” for substrate cleavage by the DNA repair endonuclease APE-1 Oezguen, Numan; Schein, Catherine H.; Peddi, Srinivasa R. Proteins: Structure, Function, and Bioinformatics, Vol. 68, Issue 1 https://doi.org/10.1002/prot.21397	journal	April 2007
Site-directed Mutagenesis of the Catalytic Residues of Bovine Pancreatic Deoxyribonuclease I Jones, Stephen J.; Worrall, Andrew F.; Connolly, Bernard A. Journal of Molecular Biology, Vol. 264, Issue 5 https://doi.org/10.1006/jmbi.1996.0703	journal	December 1996
The role of Mg2+ and specific amino acid residues in the catalytic reaction of the major human abasic endonuclease: new insights from EDTA-resistant incision of acyclic abasic site analogs and site-directed mutagenesis Erzberger, Jan P.; Wilson, David M. Journal of Molecular Biology, Vol. 290, Issue 2 https://doi.org/10.1006/jmbi.1999.2888	journal	July 1999
Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease Nguyen, Lam H.; Barsky, Daniel; Erzberger, Jan P. Journal of Molecular Biology, Vol. 298, Issue 3 https://doi.org/10.1006/jmbi.2000.3653	journal	May 2000
Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, ape1: implications for the catalytic mechanism 1 1Edited by I. A. Wilson Beernink, Peter T.; Segelke, Brent W.; Hadi, Masood Z. Journal of Molecular Biology, Vol. 307, Issue 4 https://doi.org/10.1006/jmbi.2001.4529	journal	April 2001
Chemical shift assignments for human apurinic/apyrimidinic endonuclease 1 Manvilla, Brittney A.; Varney, Kristen M.; Drohat, Alexander C. Biomolecular NMR Assignments, Vol. 4, Issue 1 https://doi.org/10.1007/s12104-009-9196-y	journal	November 2009
Apurinic sites as mutagenic intermediates Loeb, Lawrence A. Cell, Vol. 40, Issue 3 https://doi.org/10.1016/0092-8674(85)90191-6	journal	March 1985
Removal by human apurinic/apyrimidinic endonuclease 1 (Ape 1) and Escherichia coli exonuclease III of 3′-phosphoglycolates from DNA treated with neocarzinostatin, calicheamicin, and γ-radiation Chaudhry, M. Ahmad; Dedon, Peter C.; Wilson, David M. Biochemical Pharmacology, Vol. 57, Issue 5 https://doi.org/10.1016/S0006-2952(98)00327-X	journal	March 1999
Purification and characterization of an apurinic/apyrimidinic endonuclease from HeLa cells. Kane, C. M.; Linn, S. Journal of Biological Chemistry, Vol. 256, Issue 7 https://doi.org/10.1016/S0021-9258(19)69623-7	journal	April 1981
Investigation of the Role of the Histidine–Aspartate Pair in the Human Exonuclease III-like Abasic Endonuclease, Ape1 Lowry, David F.; Hoyt, David W.; Khazi, Fayaz A. Journal of Molecular Biology, Vol. 329, Issue 2 https://doi.org/10.1016/S0022-2836(03)00382-6	journal	May 2003
Functionally unrelated signalling proteins contain a fold similar to Mg2+-dependent endonucleases Dlakić, Mensur Trends in Biochemical Sciences, Vol. 25, Issue 6 https://doi.org/10.1016/S0968-0004(00)01582-6	journal	June 2000
Metals in biology: defining metalloproteomes Yannone, Steven M.; Hartung, Sophia; Menon, Angeli L. Current Opinion in Biotechnology, Vol. 23, Issue 1 https://doi.org/10.1016/j.copbio.2011.11.005	journal	February 2012
Human AP endonuclease 1 (APE1): From mechanistic insights to druggable target in cancer Abbotts, Rachel; Madhusudan, Srinivasan Cancer Treatment Reviews, Vol. 36, Issue 5 https://doi.org/10.1016/j.ctrv.2009.12.006	journal	August 2010
A Vital Role for Ape1/Ref1 Protein in Repairing Spontaneous DNA Damage in Human Cells Fung, Hua; Demple, Bruce Molecular Cell, Vol. 17, Issue 3 https://doi.org/10.1016/j.molcel.2004.12.029	journal	February 2005
Ribozyme-catalyzed and nonenzymic reactions of phosphate diesters: rate effects upon substitution of sulfur for a nonbridging phosphoryl oxygen atom Herschlag, Daniel; Piccirilli, Joseph A.; Cech, Thomas R. Biochemistry, Vol. 30, Issue 20 https://doi.org/10.1021/bi00234a003	journal	May 1991
NMR Studies Reveal an Unexpected Binding Site for a Redox Inhibitor of AP Endonuclease 1 Manvilla, Brittney A.; Wauchope, Orrette; Seley-Radtke, Katherine L. Biochemistry, Vol. 50, Issue 48 https://doi.org/10.1021/bi201071g	journal	December 2011
The Structure of Human DNase I Bound to Magnesium and Phosphate Ions Points to a Catalytic Mechanism Common to Members of the DNase I-like Superfamily Parsiegla, Goetz; Noguere, Christophe; Santell, Lydia Biochemistry, Vol. 51, Issue 51 https://doi.org/10.1021/bi300873f	journal	December 2012
Characterization of Mg ²⁺ Binding to the DNA Repair Protein Apurinic/Apyrimidic Endonuclease 1 via Solid-State ²⁵ Mg NMR Spectroscopy Lipton, A. S.; Heck, R. W.; Primak, S. Journal of the American Chemical Society, Vol. 130, Issue 29 https://doi.org/10.1021/ja0776881	journal	July 2008
Structure of DNase I at 2.0 Å resolution suggests a mechanism for binding to and cutting DNA Suck, Dietrich; Oefner, Christian Nature, Vol. 321, Issue 6070 https://doi.org/10.1038/321620a0	journal	June 1986
DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination Mol, Clifford D.; Izumi, Tadahide; Mitra, Sankar Nature, Vol. 403, Issue 6768 https://doi.org/10.1038/35000249	journal	January 2000
Instability and decay of the primary structure of DNA Lindahl, Tomas Nature, Vol. 362, Issue 6422 https://doi.org/10.1038/362709a0	journal	April 1993
Structure and function of the multifunctional DNA-repair enzyme exonuclease III Mol, Clifford D.; Kuo, Che-Fu; Thayer, Maria M. Nature, Vol. 374, Issue 6520 https://doi.org/10.1038/374381a0	journal	March 1995
Bleomycins: towards better therapeutics Chen, Jingyang; Stubbe, JoAnne Nature Reviews Cancer, Vol. 5, Issue 2 https://doi.org/10.1038/nrc1547	journal	February 2005
Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1 Barzilay, Gil; Mol, Clifford D.; Robson, Craig N. Nature Structural Biology, Vol. 2, Issue 7 https://doi.org/10.1038/nsb0795-561	journal	July 1995
Two essential but distinct functions of the mammalian abasic endonuclease Izumi, T.; Brown, D. B.; Naidu, C. V. Proceedings of the National Academy of Sciences, Vol. 102, Issue 16 https://doi.org/10.1073/pnas.0500986102	journal	April 2005
Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Demple, B.; Herman, T.; Chen, D. S. Proceedings of the National Academy of Sciences, Vol. 88, Issue 24 https://doi.org/10.1073/pnas.88.24.11450	journal	December 1991
The redox/DNA repair protein, Ref-1, is essential for early embryonic development in mice. Xanthoudakis, S.; Smeyne, R. J.; Wallace, J. D. Proceedings of the National Academy of Sciences, Vol. 93, Issue 17 https://doi.org/10.1073/pnas.93.17.8919	journal	August 1996
Distinct Roles of Ape1 Protein in the Repair of DNA Damage Induced by Ionizing Radiation or Bleomycin Fung, Hua; Demple, Bruce Journal of Biological Chemistry, Vol. 286, Issue 7 https://doi.org/10.1074/jbc.M110.146498	journal	November 2010
Biochemical Characterization of Human Tyrosyl-DNA Phosphodiesterase 2 (TDP2/TTRAP) Gao, Rui; Huang, Shar-yin N.; Marchand, Christophe Journal of Biological Chemistry, Vol. 287, Issue 36 https://doi.org/10.1074/jbc.M112.393983	journal	August 2012
Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes Tsutakawa, Susan E.; Shin, David S.; Mol, Clifford D. Journal of Biological Chemistry, Vol. 288, Issue 12 https://doi.org/10.1074/jbc.M112.422774	journal	January 2013
Pre-steady-state Kinetic Characterization of the AP Endonuclease Activity of Human AP Endonuclease 1 Maher, Robyn L.; Bloom, Linda B. Journal of Biological Chemistry, Vol. 282, Issue 42 https://doi.org/10.1074/jbc.M704341200	journal	August 2007
Transcriptional Regulatory Functions of Mammalian AP-Endonuclease (APE1/Ref-1), an Essential Multifunctional Protein Bhakat, Kishor K.; Mantha, Anil K.; Mitra, Sankar Antioxidants & Redox Signaling, Vol. 11, Issue 3 https://doi.org/10.1089/ars.2008.2198	journal	March 2009
Deletion analysis of human AP-endonuclease: minimum sequence required for the endonuclease activity Izumi, T. Carcinogenesis, Vol. 19, Issue 3 https://doi.org/10.1093/carcin/19.3.525	journal	March 1998
Requirement for human AP endonuclease 1 for repair of 3′-blocking damage at DNA single-strand breaks induced by reactive oxygen species Izumi, Tadahide; Hazra, Tapas K.; Boldogh, Istvan Carcinogenesis, Vol. 21, Issue 7 https://doi.org/10.1093/carcin/21.7.1329	journal	July 2000
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites Gorman, M. A. The EMBO Journal, Vol. 16, Issue 21 https://doi.org/10.1093/emboj/16.21.6548	journal	November 1997
Isolation of cDNA clones encoding a human apurini/apyrimidinic endonuclease that corects DNA repair and mutagenisis defects in E.coli xth (exonuclease III) mutants Robson, Craig N.; Hickson, Ian D. Nucleic Acids Research, Vol. 19, Issue 20 https://doi.org/10.1093/nar/19.20.5519	journal	January 1991
Two distinct human DNA diesterases that hydrolyze 3′-blocking deoxyribose fragments from oxidized DNA Chen, Davis S.; Herman, Tory; Demple, Bruce Nucleic Acids Research, Vol. 19, Issue 21 https://doi.org/10.1093/nar/19.21.5907	journal	January 1991
Asparagine 212 is essential for abasic site recognition by the human DNA repair endonuclease HAP1 Rothwell, D. Nucleic Acids Research, Vol. 24, Issue 21 https://doi.org/10.1093/nar/24.21.4217	journal	November 1996
Substitution of Asp-210 in HAP1 (APE/Ref-1) eliminates endonuclease activity but stabilises substrate binding Rothwell, D. G. Nucleic Acids Research, Vol. 28, Issue 11 https://doi.org/10.1093/nar/28.11.2207	journal	June 2000
APE1 is the major 3'-phosphoglycolate activity in human cell extracts Parsons, J. L. Nucleic Acids Research, Vol. 32, Issue 12 https://doi.org/10.1093/nar/gkh676	journal	July 2004
Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family Castillo-Acosta, V. M.; Ruiz-Perez, L. M.; Yang, W. Nucleic Acids Research, Vol. 37, Issue 6 https://doi.org/10.1093/nar/gkp021	journal	January 2009
PROCHECK: a program to check the stereochemical quality of protein structures Laskowski, R. A.; MacArthur, M. W.; Moss, D. S. Journal of Applied Crystallography, Vol. 26, Issue 2 https://doi.org/10.1107/S0021889892009944	journal	April 1993
Use of TLS parameters to model anisotropic displacements in macromolecular refinement Winn, M. D.; Isupov, M. N.; Murshudov, G. N. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 1 https://doi.org/10.1107/S0907444900014736	journal	January 2001
Geometry of metal–ligand interactions in proteins Harding, Marjorie M. Acta Crystallographica Section D Biological Crystallography, Vol. 57, Issue 3 https://doi.org/10.1107/S0907444900019168	journal	March 2001
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Likelihood-enhanced fast translation functions McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Storoni, Laurent C. Acta Crystallographica Section D Biological Crystallography, Vol. 61, Issue 4 https://doi.org/10.1107/S0907444905001617	journal	March 2005
Small revisions to predicted distances around metal sites in proteins Harding, Marjorie M. Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 6 https://doi.org/10.1107/S0907444906014594	journal	May 2006
An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S090744491003982X	journal	March 2011
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
A proficient enzyme Radzicka, A.; Wolfenden, R. Science, Vol. 267, Issue 5194 https://doi.org/10.1126/science.7809611	journal	January 1995
Repair of Oxidative Damage to DNA: Enzymology and Biology Demple, B.; Harrison, L. Annual Review of Biochemistry, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.bi.63.070194.004411	journal	June 1994
Inhibition of Ape1 nuclease activity by lead, iron, and cadmium. McNeill, Daniel R.; Narayana, Avinash; Wong, Heng-Kuan Environmental Health Perspectives, Vol. 112, Issue 7 https://doi.org/10.1289/ehp.7038	journal	May 2004
Targeting Base Excision Repair for Chemosensitization Adhikari, Sanjay; Choudhury, Sujata; Mitra, Partha Anti-Cancer Agents in Medicinal Chemistry, Vol. 8, Issue 4 https://doi.org/10.2174/187152008784220366	journal	May 2008
MD simulation and experimental evidence for Mg2+ binding at the b site in human AP endonuclease 1 Oezguen, Numan; Mantha, Anil K.; Izumi, Tadahide Bioinformation, Vol. 7, Issue 4 https://doi.org/10.6026/97320630007184	journal	October 2011

Cited By (10)

Incorporation of omics analyses into artificial gravity research for space exploration countermeasure development Schmidt, Michael A.; Goodwin, Thomas J.; Pelligra, Ralph Metabolomics, Vol. 12, Issue 2 https://doi.org/10.1007/s11306-015-0942-0	journal	January 2016
Structural comparison of AP endonucleases from the exonuclease III family reveals new amino acid residues in human AP endonuclease 1 that are involved in incision of damaged DNA Redrejo-Rodríguez, Modesto; Vigouroux, Armelle; Mursalimov, Aibek Biochimie, Vol. 128-129 https://doi.org/10.1016/j.biochi.2016.06.011	journal	September 2016
High-Resolution Crystal Structures Reveal Plasticity in the Metal Binding Site of Apurinic/Apyrimidinic Endonuclease I He, Hongzhen; Chen, Qiujia; Georgiadis, Millie M. Biochemistry, Vol. 53, Issue 41 https://doi.org/10.1021/bi500676p	journal	October 2014
Capturing snapshots of APE1 processing DNA damage Freudenthal, Bret D.; Beard, William A.; Cuneo, Matthew J. Nature Structural & Molecular Biology, Vol. 22, Issue 11 https://doi.org/10.1038/nsmb.3105	journal	October 2015
Substrate specificity of human apurinic/apyrimidinic endonuclease APE1 in the nucleotide incision repair pathway Kuznetsova, Alexandra A.; Matveeva, Anna G.; Milov, Alexander D. Nucleic Acids Research, Vol. 46, Issue 21 https://doi.org/10.1093/nar/gky912	journal	October 2018
Cloning and Characterization of a Wheat Homologue of Apurinic/Apyrimidinic Endonuclease Ape1L Joldybayeva, Botagoz; Prorok, Paulina; Grin, Inga R. PLoS ONE, Vol. 9, Issue 3 https://doi.org/10.1371/journal.pone.0092963	journal	March 2014
Insights into Mechanisms of Damage Recognition and Catalysis by APE1-like Enzymes Bulygin, Anatoly A.; Fedorova, Olga S.; Kuznetsov, Nikita A. International Journal of Molecular Sciences, Vol. 23, Issue 8 https://doi.org/10.3390/ijms23084361	journal	April 2022
Kinetic Features of 3′-5′ Exonuclease Activity of Human AP-Endonuclease APE1 Kuznetsova, Alexandra; Fedorova, Olga; Kuznetsov, Nikita Molecules, Vol. 23, Issue 9 https://doi.org/10.3390/molecules23092101	journal	August 2018
Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1 Miroshnikova, Anastasia D.; Kuznetsova, Alexandra A.; Vorobjev, Yuri N. Molecular BioSystems, Vol. 12, Issue 5 https://doi.org/10.1039/c6mb00128a	journal	January 2016
Structure-based virtual screening toward the discovery of novel inhibitors of the DNA repair activity of the human apurinic/apyrimidinic endonuclease 1 Guerreiro, Patrícia S.; Estácio, Sílvia G.; Antunes, Fernando Chemical Biology & Drug Design, Vol. 88, Issue 6 https://doi.org/10.1111/cbdd.12826	journal	September 2016

Similar Records

DNA Apurinic-Apyrimidinic Site Binding And Excision By Endonuclease IV

Journal Article · Mon May 18 00:00:00 EDT 2009 · Nature Struct. Biol 15:515,2008 · OSTI ID:953156

Conserved structural chemistry for incision activity in structurally non-homologous apurinic/apyrimidinic endonuclease APE1 and endonuclease IV DNA repair enzymes.

Journal Article · Fri Mar 22 00:00:00 EDT 2013 · Journal of Biological Chemistry · OSTI ID:1170766

Human endonuclease specific for apurinic/apyrimidinic sites in DNA

Journal Article · Fri Dec 31 23:00:00 EST 1976 · J. Biol. Chem.; (United States) · OSTI ID:5063728

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biophysics
Crystallography