8IGI
 
 | | Crystal structure of HP1526 (XthA)- a base excision DNA repair protein in Helicobacter pylori | | Descriptor: | 1,3-BUTANEDIOL, Exodeoxyribonuclease (LexA), MANGANESE (II) ION | | Authors: | Dinh, T.T, Dao, O, Lee, K.H. | | Deposit date: | 2023-02-20 | | Release date: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Crystal structure of the apurinic/apyrimidinic endonuclease XthA (HP1526 protein) from Helicobacter pylori.
Biochem.Biophys.Res.Commun., 663, 2023
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8J2F
 | | Human neutral shpingomyelinase | | Descriptor: | HEPTANE, MAGNESIUM ION, Sphingomyelin phosphodiesterase 2, ... | | Authors: | Zhang, S.S. | | Deposit date: | 2023-04-14 | | Release date: | 2023-12-06 | | Method: | ELECTRON MICROSCOPY (3.07 Å) | | Cite: | Molecular basis for the catalytic mechanism of human neutral sphingomyelinases 1 (hSMPD2)
Nat Commun, 14, 2023
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8KA5
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7CD6
 | | mAPE1-recessed dsDNA product complex | | Descriptor: | DNA (5'-D(*GP*CP*GP*TP*AP*AP*TP*AP*C)-3'), DNA-(apurinic or apyrimidinic site) endonuclease | | Authors: | Liu, T.C, Hsiao, Y.Y. | | Deposit date: | 2020-06-18 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.701 Å) | | Cite: | APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.
Nat Commun, 12, 2021
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7CD5
 | | mAPE1-blunt-ended dsDNA product complex | | Descriptor: | DNA(5'-D(*CP*GP*TP*AP*AP*TP*AP*CP*G)-3'), DNA-(apurinic or apyrimidinic site) endonuclease | | Authors: | Liu, T.C, Hsiao, Y.Y. | | Deposit date: | 2020-06-18 | | Release date: | 2021-01-13 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.
Nat Commun, 12, 2021
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7CNE
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8KA3
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8KA4
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3TEB
 | | endonuclease/exonuclease/phosphatase family protein from Leptotrichia buccalis C-1013-b | | Descriptor: | Endonuclease/exonuclease/phosphatase, MAGNESIUM ION | | Authors: | Chang, C, Bigelow, L, Muniez, I, Bearden, J, Joachimiak, A, Midwest Center for Structural Genomics (MCSG) | | Deposit date: | 2011-08-12 | | Release date: | 2011-08-31 | | Method: | X-RAY DIFFRACTION (2.99 Å) | | Cite: | Crystal structure of endonuclease/exonuclease/phosphatase family protein from Leptotrichia buccalis C-1013-b
To be Published
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3U8U
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7KIU
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7LPH
 | | APE1 Mn-bound product complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (1.99 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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7LPJ
 | | APE1 Mn-bound phosphorothioate substrate complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase, ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.56 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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7LPG
 | | APE1 product complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-R(P*N)-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), ... | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.08 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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7LPI
 | | APE1 phosphorothioate substrate complex with abasic ribonucleotide DNA | | Descriptor: | DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-R(P*(YA4))-D(P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3'), DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA-(apurinic or apyrimidinic site) lyase | | Authors: | Freudenthal, B.D, Hoitsma, N.M. | | Deposit date: | 2021-02-11 | | Release date: | 2021-08-04 | | Last modified: | 2023-10-18 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Altered APE1 activity on abasic ribonucleotides is mediated by changes in the nucleoside sugar pucker.
Comput Struct Biotechnol J, 19, 2021
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3W2X
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3W2Y
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2F1N
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6NF0
 | | Nocturnin with bound NADPH substrate | | Descriptor: | CALCIUM ION, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, Nocturnin | | Authors: | Estrella, M.A, Du, J, Korennykh, A. | | Deposit date: | 2018-12-18 | | Release date: | 2019-05-01 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | The metabolites NADP+and NADPH are the targets of the circadian protein Nocturnin (Curled).
Nat Commun, 10, 2019
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1DE9
 | | HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION | | Descriptor: | 5'-d(*CP*TP*AP*C)-3', 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3', 5'-d(P*(3DR)P*GP*AP*TP*C)-3', ... | | Authors: | Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A. | | Deposit date: | 1999-11-13 | | Release date: | 2000-02-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Nature, 403, 2000
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1DEW
 | | CRYSTAL STRUCTURE OF HUMAN APE1 BOUND TO ABASIC DNA | | Descriptor: | 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3', 5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3', MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE, ... | | Authors: | Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A. | | Deposit date: | 1999-11-15 | | Release date: | 2000-02-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.65 Å) | | Cite: | DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination
Nature, 403, 2000
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1DE8
 | | HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA | | Descriptor: | DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)-3'), MAJOR APURINIC/APYRIMIDINIC ENDONUCLEASE | | Authors: | Mol, C.D, Izumi, T, Mitra, S, Tainer, J.A. | | Deposit date: | 1999-11-13 | | Release date: | 2000-02-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.95 Å) | | Cite: | DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected
Nature, 403, 2000
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1DNK
 | | THE X-RAY STRUCTURE OF THE DNASE I-D(GGTATACC)2 COMPLEX AT 2.3 ANGSTROMS RESOLUTION | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DNA (5'-D(*GP*GP*TP*AP*TP*AP*C)-3'), DNA (5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3'), ... | | Authors: | Weston, S.A, Lahm, A, Suck, D. | | Deposit date: | 1992-08-10 | | Release date: | 1994-01-31 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
J.Mol.Biol., 226, 1992
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1E9N
 | | A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism | | Descriptor: | DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, LEAD (II) ION | | Authors: | Beernink, P.T, Segelke, B.W, Rupp, B. | | Deposit date: | 2000-10-24 | | Release date: | 2001-02-16 | | Last modified: | 2019-05-08 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
J.Mol.Biol., 307, 2001
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6P93
 | | Human APE1 K98A AP-endonuclease product complex | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Whitaker, A.W, Stark, W.J, Freudenthal, B.D. | | Deposit date: | 2019-06-09 | | Release date: | 2020-01-01 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance.
Mutagenesis, 35, 2020
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