Published in J Biol Chem on January 25, 2013
Human apurinic/apyrimidinic endonuclease 1. Antioxid Redox Signal (2013) 1.34
Envisioning the dynamics and flexibility of Mre11-Rad50-Nbs1 complex to decipher its roles in DNA replication and repair. Prog Biophys Mol Biol (2015) 1.07
The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once. DNA Repair (Amst) (2014) 1.04
Emerging critical roles of Fe-S clusters in DNA replication and repair. Biochim Biophys Acta (2015) 0.96
Transient-state kinetics of apurinic/apyrimidinic (AP) endonuclease 1 acting on an authentic AP site and commonly used substrate analogs: the effect of diverse metal ions and base mismatches. Biochemistry (2013) 0.84
Capturing snapshots of APE1 processing DNA damage. Nat Struct Mol Biol (2015) 0.84
Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor. Acta Crystallogr D Biol Crystallogr (2013) 0.82
Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases. Proc Natl Acad Sci U S A (2013) 0.82
The structure of phosphoinositide phosphatases: Insights into substrate specificity and catalysis. Biochim Biophys Acta (2014) 0.80
Cloning and characterization of a wheat homologue of apurinic/apyrimidinic endonuclease Ape1L. PLoS One (2014) 0.79
High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I. Biochemistry (2014) 0.79
Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair. PLoS One (2015) 0.77
Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. Archaea (2014) 0.77
3CAPS - a structural AP-site analogue as a tool to investigate DNA base excision repair. Nucleic Acids Res (2016) 0.75
Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family. Biochemistry (2016) 0.75
Thermodynamics of Damaged DNA Binding and Catalysis by Human AP Endonuclease 1. Acta Naturae (2016) 0.75
High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center. Nat Commun (2017) 0.75
Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr (2010) 108.52
Instability and decay of the primary structure of DNA. Nature (1993) 25.58
Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins (2006) 22.80
The DNA damage response: making it safe to play with knives. Mol Cell (2010) 16.13
Reduced surface: an efficient way to compute molecular surfaces. Biopolymers (1996) 10.62
Rapid automated molecular replacement by evolutionary search. Acta Crystallogr D Biol Crystallogr (1999) 8.97
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys J (2007) 7.99
Endonuclease IV (nfo) mutant of Escherichia coli. J Bacteriol (1986) 5.32
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature (1996) 4.46
DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]. Nature (2000) 4.40
Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell (2008) 4.26
Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc Natl Acad Sci U S A (1991) 3.82
Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli. Proc Natl Acad Sci U S A (1986) 3.72
The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature (2002) 3.48
Geometry of metal-ligand interactions in proteins. Acta Crystallogr D Biol Crystallogr (2001) 3.20
Homogeneous Escherichia coli endonuclease IV. Characterization of an enzyme that recognizes oxidative damage in DNA. J Biol Chem (1988) 3.15
Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature (1995) 3.00
Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding. Mol Cell Biol (1993) 2.73
MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily. Nat Struct Biol (1998) 2.70
Apurinic sites as mutagenic intermediates. Cell (1985) 2.63
Microbial metalloproteomes are largely uncharacterized. Nature (2010) 2.62
An exonucleolytic activity of human apurinic/apyrimidinic endonuclease on 3' mispaired DNA. Nature (2002) 2.58
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites. EMBO J (1997) 2.53
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell (2011) 2.44
The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst) (2007) 2.26
Repair of endogenous DNA damage. Cold Spring Harb Symp Quant Biol (2000) 2.24
DNA base damage recognition and removal: new twists and grooves. Mutat Res (2005) 2.21
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell (1999) 2.14
DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature (1998) 2.05
Base excision repair intermediates induce p53-independent cytotoxic and genotoxic responses. J Biol Chem (2003) 1.95
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res (2002) 1.89
Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means. Mutat Res (2000) 1.71
Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature (2009) 1.70
Identification of critical active-site residues in the multifunctional human DNA repair enzyme HAP1. Nat Struct Biol (1995) 1.68
Nickel superoxide dismutase structure and mechanism. Biochemistry (2004) 1.66
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 (2001) 1.51
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J (2003) 1.49
Evolution of the redox function in mammalian apurinic/apyrimidinic endonuclease. Mutat Res (2008) 1.47
Alternative nucleotide incision repair pathway for oxidative DNA damage. Nature (2002) 1.46
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol (2008) 1.46
A novel endonuclease mechanism directly visualized for I-PpoI. Nat Struct Biol (1999) 1.43
An equivalent metal ion in one- and two-metal-ion catalysis. Nat Struct Mol Biol (2008) 1.41
The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J Mol Biol (1992) 1.39
Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell (1999) 1.37
The active site of Serratia endonuclease contains a conserved magnesium-water cluster. J Mol Biol (1999) 1.33
Structural insights into the first incision reaction during nucleotide excision repair. EMBO J (2005) 1.30
An extracellular nuclease from Serratia marcescens. II. Specificity of the enzyme. J Biol Chem (1969) 1.27
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair. Nat Struct Mol Biol (2009) 1.26
Intragenic suppression of an active site mutation in the human apurinic/apyrimidinic endonuclease. J Mol Biol (1999) 1.26
Recognition and removal of oxidized guanines in duplex DNA by the base excision repair enzymes hOGG1, yOGG1, and yOGG2. Biochemistry (2003) 1.21
Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product. J Biol Chem (1998) 1.21
Identification of Apurinic/apyrimidinic endonuclease 1 (APE1) as the endoribonuclease that cleaves c-myc mRNA. Nucleic Acids Res (2009) 1.20
Substitution of Asp-210 in HAP1 (APE/Ref-1) eliminates endonuclease activity but stabilises substrate binding. Nucleic Acids Res (2000) 1.16
A "moving metal mechanism" for substrate cleavage by the DNA repair endonuclease APE-1. Proteins (2007) 1.16
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A (2007) 1.14
The 3'->5' exonuclease of Apn1 provides an alternative pathway to repair 7,8-dihydro-8-oxodeoxyguanosine in Saccharomyces cerevisiae. Mol Cell Biol (2005) 1.14
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc Natl Acad Sci U S A (1998) 1.13
Single-turnover and steady-state kinetics of hydrolysis of cephalosporins by beta-lactamase I from Bacillus cereus. Biochem J (1985) 1.13
Cancer, cadmium and genome integrity. Nat Genet (2003) 1.11
Characterisation of new substrate specificities of Escherichia coli and Saccharomyces cerevisiae AP endonucleases. Nucleic Acids Res (2003) 1.08
Purification and characterization of Thermotoga maritima endonuclease IV, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase. J Bacteriol (1999) 1.07
Pre-steady-state kinetic characterization of the AP endonuclease activity of human AP endonuclease 1. J Biol Chem (2007) 1.07
Single-turnover analysis of mutant human apurinic/apyrimidinic endonuclease. Biochemistry (1999) 1.05
Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases. Trends Biochem Sci (2011) 1.02
Cloning and characterization of a periplasmic nuclease of Vibrio vulnificus and its role in preventing uptake of foreign DNA. Appl Environ Microbiol (2001) 1.02
Asparagine 212 is essential for abasic site recognition by the human DNA repair endonuclease HAP1. Nucleic Acids Res (1996) 1.01
Characterization of an endonuclease IV 3'-5' exonuclease activity. J Biol Chem (2002) 0.98
Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV. J Mol Biol (2004) 0.94
Unusual role of a cysteine residue in substrate binding and activity of human AP-endonuclease 1. J Mol Biol (2008) 0.94
Novel role of tyrosine in catalysis by human AP endonuclease 1. DNA Repair (Amst) (2004) 0.94
Understanding the effect of magnesium ion concentration on the catalytic activity of ribonuclease H through computation: does a third metal binding site modulate endonuclease catalysis? J Am Chem Soc (2010) 0.92
Enzymatic mechanism of human apurinic/apyrimidinic endonuclease against a THF AP site model substrate. Biochemistry (2009) 0.91
Neutralizing mutations of carboxylates that bind metal 2 in T5 flap endonuclease result in an enzyme that still requires two metal ions. J Biol Chem (2011) 0.89
Investigation of the role of the histidine-aspartate pair in the human exonuclease III-like abasic endonuclease, Ape1. J Mol Biol (2003) 0.86
Characterization of Mg2+ binding to the DNA repair protein apurinic/apyrimidic endonuclease 1 via solid-state 25Mg NMR spectroscopy. J Am Chem Soc (2008) 0.86
MD simulation and experimental evidence for Mg²+ binding at the B site in human AP endonuclease 1. Bioinformation (2011) 0.80
Identification of a residue critical for the excision of 3'-blocking ends in apurinic/apyrimidinic endonucleases of the Xth family. Nucleic Acids Res (2009) 0.80
[DNA-(N4-cytosine)-methyltransferase from Bacillus amyloliquefaciens: kinetic and substrate binding properties]. Mol Biol (Mosk) (2001) 0.79
Structure of the endonuclease IV homologue from Thermotoga maritima in the presence of active-site divalent metal ions. Acta Crystallogr Sect F Struct Biol Cryst Commun (2010) 0.77
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science (2010) 10.30
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys (2007) 9.07
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods (2009) 6.77
Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science (2009) 4.41
Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol (2004) 4.29
Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Cell (2008) 4.26
Overcoming mutation-based resistance to antiandrogens with rational drug design. Elife (2013) 3.49
Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells. Cell Res (2008) 3.48
The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair. Nature (2002) 3.48
AP endonuclease-independent DNA base excision repair in human cells. Mol Cell (2004) 3.37
Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell (2006) 3.36
Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proc Natl Acad Sci U S A (2002) 3.33
Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell (2004) 3.33
Accurate assessment of mass, models and resolution by small-angle scattering. Nature (2013) 3.18
XPD helicase structures and activities: insights into the cancer and aging phenotypes from XPD mutations. Cell (2008) 3.14
Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem Cell Biol (2007) 3.13
Full-length archaeal Rad51 structure and mutants: mechanisms for RAD51 assembly and control by BRCA2. EMBO J (2003) 2.95
The minimum crystal size needed for a complete diffraction data set. Acta Crystallogr D Biol Crystallogr (2010) 2.94
Nbs1 flexibly tethers Ctp1 and Mre11-Rad50 to coordinate DNA double-strand break processing and repair. Cell (2009) 2.90
Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law. Biopolymers (2011) 2.87
DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol (2004) 2.86
Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges. Science (2012) 2.80
Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell (2003) 2.78
SUMO-targeted ubiquitin ligases in genome stability. EMBO J (2007) 2.77
Microbial metalloproteomes are largely uncharacterized. Nature (2010) 2.62
Early abscisic acid signal transduction mechanisms: newly discovered components and newly emerging questions. Genes Dev (2010) 2.60
Identification and characterization of a novel human DNA glycosylase for repair of cytosine-derived lesions. J Biol Chem (2002) 2.54
Repair of oxidized bases in DNA bubble structures by human DNA glycosylases NEIL1 and NEIL2. J Biol Chem (2003) 2.53
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol (2010) 2.45
Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily. Cell (2011) 2.44
ROS generated by pollen NADPH oxidase provide a signal that augments antigen-induced allergic airway inflammation. J Clin Invest (2005) 2.34
ATM regulates Mre11-dependent DNA end-degradation and microhomology-mediated end joining. Cell Cycle (2010) 2.32
Boc is a receptor for sonic hedgehog in the guidance of commissural axons. Nature (2006) 2.29
Structural basis for isozyme-specific regulation of electron transfer in nitric-oxide synthase. J Biol Chem (2004) 2.28
Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage. EMBO J (2006) 2.27
Two essential but distinct functions of the mammalian abasic endonuclease. Proc Natl Acad Sci U S A (2005) 2.26
The intricate structural chemistry of base excision repair machinery: implications for DNA damage recognition, removal, and repair. DNA Repair (Amst) (2007) 2.26
A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell (2006) 2.23
DNA base damage recognition and removal: new twists and grooves. Mutat Res (2005) 2.21
The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome. Cell Cycle (2011) 2.15
Conserved XPB core structure and motifs for DNA unwinding: implications for pathway selection of transcription or excision repair. Mol Cell (2006) 2.13
Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell (2003) 2.11
A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem Sci (2008) 2.05
Mre11-Rad50-Nbs1 conformations and the control of sensing, signaling, and effector responses at DNA double-strand breaks. DNA Repair (Amst) (2010) 1.96
Role of acetylated human AP-endonuclease (APE1/Ref-1) in regulation of the parathyroid hormone gene. EMBO J (2003) 1.94
Rad50/SMC proteins and ABC transporters: unifying concepts from high-resolution structures. Curr Opin Struct Biol (2003) 1.93
Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex. J Biol Chem (2009) 1.91
MDB: the Metalloprotein Database and Browser at The Scripps Research Institute. Nucleic Acids Res (2002) 1.89
Recognition of RNA polymerase II and transcription bubbles by XPG, CSB, and TFIIH: insights for transcription-coupled repair and Cockayne Syndrome. Mol Cell (2005) 1.89
Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J (2013) 1.83
ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. J Mol Biol (2003) 1.82
Transcriptional regulatory functions of mammalian AP-endonuclease (APE1/Ref-1), an essential multifunctional protein. Antioxid Redox Signal (2009) 1.81
Hexameric structures of the archaeal secretion ATPase GspE and implications for a universal secretion mechanism. EMBO J (2007) 1.77
The discovery of a new family of mammalian enzymes for repair of oxidatively damaged DNA, and its physiological implications. Carcinogenesis (2003) 1.77
DNA charge transport as a first step in coordinating the detection of lesions by repair proteins. Proc Natl Acad Sci U S A (2012) 1.71
A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation. DNA Repair (Amst) (2010) 1.71
Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature (2009) 1.70
Tumor-derived hydrogen sulfide, produced by cystathionine-β-synthase, stimulates bioenergetics, cell proliferation, and angiogenesis in colon cancer. Proc Natl Acad Sci U S A (2013) 1.69
Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. J Appl Crystallogr (2013) 1.69
DNA double-strand break repair from head to tail. Curr Opin Struct Biol (2002) 1.67
ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Nat Struct Mol Biol (2011) 1.66
Nickel superoxide dismutase structure and mechanism. Biochemistry (2004) 1.66
Interaction of the human DNA glycosylase NEIL1 with proliferating cell nuclear antigen. The potential for replication-associated repair of oxidized bases in mammalian genomes. J Biol Chem (2007) 1.63
Improving small-angle X-ray scattering data for structural analyses of the RNA world. RNA (2010) 1.60
Oxidative stress: an essential factor in the pathogenesis of gastrointestinal mucosal diseases. Physiol Rev (2014) 1.57
WRN exonuclease structure and molecular mechanism imply an editing role in DNA end processing. Nat Struct Mol Biol (2006) 1.55
Mammalian DNA base excision repair proteins: their interactions and role in repair of oxidative DNA damage. Toxicology (2003) 1.52
Switching on kinases: oncogenic activation of BRAF and the PDGFR family. Nat Rev Cancer (2004) 1.49
XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair. J Biol Chem (2011) 1.48
Acetylation of human 8-oxoguanine-DNA glycosylase by p300 and its role in 8-oxoguanine repair in vivo. Mol Cell Biol (2006) 1.48
Protein mimicry of DNA and pathway regulation. DNA Repair (Amst) (2005) 1.46
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat Struct Mol Biol (2008) 1.46
NEIL2-initiated, APE-independent repair of oxidized bases in DNA: Evidence for a repair complex in human cells. DNA Repair (Amst) (2006) 1.45
XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase. DNA Repair (Amst) (2011) 1.45