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Title: Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC

Authors:
ORCiD logo [1];  [1];  [1];  [2];  [2];  [2];  [1]; ORCiD logo [1]
  1. Department of Biological Sciences Vanderbilt University Nashville TN USA
  2. Department of Chemistry University of California Davis CA USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1547116
Grant/Contract Number:  
DE‐AC02‐06CH11357
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
EMBO Journal
Additional Journal Information:
Journal Name: EMBO Journal Journal Volume: 37 Journal Issue: 1; Journal ID: ISSN 0261-4189
Publisher:
EMBO
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Shi, Rongxin, Mullins, Elwood A., Shen, Xing‐Xing, Lay, Kori T., Yuen, Philip K., David, Sheila S., Rokas, Antonis, and Eichman, Brandt F.. Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC. United Kingdom: N. p., 2017. Web. doi:10.15252/embj.201797833.
Shi, Rongxin, Mullins, Elwood A., Shen, Xing‐Xing, Lay, Kori T., Yuen, Philip K., David, Sheila S., Rokas, Antonis, & Eichman, Brandt F.. Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC. United Kingdom. https://doi.org/10.15252/embj.201797833
Shi, Rongxin, Mullins, Elwood A., Shen, Xing‐Xing, Lay, Kori T., Yuen, Philip K., David, Sheila S., Rokas, Antonis, and Eichman, Brandt F.. Fri . "Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC". United Kingdom. https://doi.org/10.15252/embj.201797833.
@article{osti_1547116,
title = {Selective base excision repair of DNA damage by the non‐base‐flipping DNA glycosylase AlkC},
author = {Shi, Rongxin and Mullins, Elwood A. and Shen, Xing‐Xing and Lay, Kori T. and Yuen, Philip K. and David, Sheila S. and Rokas, Antonis and Eichman, Brandt F.},
abstractNote = {},
doi = {10.15252/embj.201797833},
journal = {EMBO Journal},
number = 1,
volume = 37,
place = {United Kingdom},
year = {2017},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.15252/embj.201797833

Citation Metrics:
Cited by: 15 works
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Works referenced in this record:

Recent advances in the structural mechanisms of DNA glycosylases
journal, January 2013

  • Brooks, Sonja C.; Adhikary, Suraj; Rubinson, Emily H.
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1834, Issue 1
  • DOI: 10.1016/j.bbapap.2012.10.005

Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli
journal, September 2004

  • Delaney, J. C.; Essigmann, J. M.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 39
  • DOI: 10.1073/pnas.0403489101

An unprecedented nucleic acid capture mechanism for excision of DNA damage
journal, October 2010

  • Rubinson, Emily H.; Gowda, A. S. Prakasha; Spratt, Thomas E.
  • Nature, Vol. 468, Issue 7322
  • DOI: 10.1038/nature09428

Structure of the sporulation-specific transcription factor Ndt80 bound to DNA
journal, November 2002


Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
journal, May 2009

  • Zheng, G.; Lu, X. -J.; Olson, W. K.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp358

Dali server update
journal, April 2016

  • Holm, Liisa; Laakso, Laura M.
  • Nucleic Acids Research, Vol. 44, Issue W1
  • DOI: 10.1093/nar/gkw357

Structure of the human NF-kappa B p52 homodimer-DNA complex at 2.1Aresolution
journal, December 1997


Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA
journal, March 2007


Collaboration gets the most out of software
journal, September 2013


Escherichia coil , Saccharomyces cerevisiae , rat and human 3-methyladenine DNA glycosylases repair 1, N 6 -ethenoadenine when present in DNA
journal, January 1995

  • Saparbaev, Murat; Kleibl, Karol; Laval, Jacques
  • Nucleic Acids Research, Vol. 23, Issue 18
  • DOI: 10.1093/nar/23.18.3750

A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD
journal, August 2008

  • Rubinson, Emily H.; Metz, Audrey H.; O'Quin, Jami
  • Journal of Molecular Biology, Vol. 381, Issue 1
  • DOI: 10.1016/j.jmb.2008.05.078

Two DNA glycosylases in E. coli which release primarily 3-methyladenine
journal, March 1982

  • Thomas, Loretta; Yang, Chul Hak; Goldthwait, David A.
  • Biochemistry, Vol. 21, Issue 6
  • DOI: 10.1021/bi00535a009

The immunoglobulin superfamily: An insight on its tissular, species, and functional diversity
journal, April 1998

  • Halaby, D. M.; Mornon, J. P. E.
  • Journal of Molecular Evolution, Vol. 46, Issue 4
  • DOI: 10.1007/PL00006318

The immunoglobulin fold family: sequence analysis and 3D structure comparisons
journal, July 1999

  • Halaby, D. M.; Poupon, A.; Mornon, J. -P.
  • Protein Engineering, Design and Selection, Vol. 12, Issue 7
  • DOI: 10.1093/protein/12.7.563

DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the AlkA enzyme in Escherichia coli.
journal, January 1994


A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures
journal, July 2013

  • Backe, Paul H.; Simm, Roger; Laerdahl, Jon K.
  • Journal of Structural Biology, Vol. 183, Issue 1
  • DOI: 10.1016/j.jsb.2013.04.007

The DNA-damage response in human biology and disease
journal, October 2009


Structural Analyses of DNA Recognition by the AML1/Runx-1 Runt Domain and Its Allosteric Control by CBFβ
journal, March 2001


MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
journal, May 2007

  • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm216

Structure–function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans
journal, May 2012

  • Moe, Elin; Hall, David R.; Leiros, Ingar
  • Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 6
  • DOI: 10.1107/S090744491200947X

Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA
journal, March 1998

  • Chen, Lin; Glover, J. N. Mark; Hogan, Patrick G.
  • Nature, Vol. 392, Issue 6671
  • DOI: 10.1038/32100

Demethylation of 3-Methylthymine in DNA by Bacterial and Human DNA Dioxygenases
journal, July 2004

  • Koivisto, Pertti; Robins, Peter; Lindahl, Tomas
  • Journal of Biological Chemistry, Vol. 279, Issue 39
  • DOI: 10.1074/jbc.M407960200

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Oxidative dealkylation DNA repair mediated by the mononuclear non-heme iron AlkB proteins
journal, April 2006


Excision of 3-methylguanine from alkylated DNA by 3-methyladenine DNA glycosylase I of Escherichia coli
journal, January 1993

  • Bjelland, Svein; Bjørås, Magnar; Seeberg, Erling
  • Nucleic Acids Research, Vol. 21, Issue 9
  • DOI: 10.1093/nar/21.9.2045

The Immunoglobulin Fold Structural Classification, Sequence Patterns and Common Core
journal, September 1994


The Escherichia coli 3-Methyladenine DNA Glycosylase AlkA Has a Remarkably Versatile Active Site
journal, May 2004

  • O'Brien, Patrick J.; Ellenberger, Tom
  • Journal of Biological Chemistry, Vol. 279, Issue 26
  • DOI: 10.1074/jbc.M403860200

Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server
journal, December 2013

  • Zheng, Heping; Chordia, Mahendra D.; Cooper, David R.
  • Nature Protocols, Vol. 9, Issue 1
  • DOI: 10.1038/nprot.2013.172

Human cDNA expressing a functional DNA glycosylase excising 3-methyladenine and 7-methylguanine
journal, May 1991

  • O'Connor, Timothy R.; Laval, Jacques
  • Biochemical and Biophysical Research Communications, Vol. 176, Issue 3
  • DOI: 10.1016/0006-291X(91)90408-Y

DNA repair: From molecular mechanism to human disease
journal, August 2006


Data publication with the structural biology data grid supports live analysis
journal, March 2016

  • Meyer, Peter A.; Socias, Stephanie; Key, Jason
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms10882

DNA bending and a flip-out mechanism for base excision by the helix–hairpin–helix DNA glycosylase, Escherichia coli AlkA
journal, February 2000

  • Hollis, Thomas; Ichikawa, Yoshitaka; Ellenberger, Tom
  • The EMBO Journal, Vol. 19, Issue 4
  • DOI: 10.1093/emboj/19.4.758

Rapid Calculation of Protein pKa Values Using Rosetta
journal, August 2012


AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli
journal, September 2002

  • Falnes, Pål Ø.; Johansen, Rune F.; Seeberg, Erling
  • Nature, Vol. 419, Issue 6903
  • DOI: 10.1038/nature01048

An HPLC–tandem mass spectrometry method for simultaneous detection of alkylated base excision repair products
journal, November 2013


Repairing DNA-methylation damage
journal, February 2004

  • Sedgwick, Barbara
  • Nature Reviews Molecular Cell Biology, Vol. 5, Issue 2
  • DOI: 10.1038/nrm1312

Base Excision Repair
journal, April 2013


A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus , AlkC and AlkD : Alkylation repair in
journal, January 2006


Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations
journal, July 1994


Substrate specificities of bacterial and human AlkB proteins
journal, June 2004


The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions
journal, October 2015

  • Mullins, Elwood A.; Shi, Rongxin; Parsons, Zachary D.
  • Nature, Vol. 527, Issue 7577
  • DOI: 10.1038/nature15728

Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes
journal, July 2011


Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
journal, May 2013


A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases
journal, May 2015


Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage
journal, September 2002

  • Trewick, Sarah C.; Henshaw, Timothy F.; Hausinger, Robert P.
  • Nature, Vol. 419, Issue 6903
  • DOI: 10.1038/nature00908

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

Methylpurine DNA Glycosylase of the Hyperthermophilic Archaeon Archaeoglobus fulgidus
journal, October 2002

  • Birkeland, Nils-Kåre; Ånensen, Hilde; Kristoffersen, Wenche
  • Biochemistry, Vol. 41, Issue 42
  • DOI: 10.1021/bi020334w

Cloning a eukaryotic DNA glycosylase repair gene by the suppression of a DNA repair defect in Escherichia coli.
journal, October 1989

  • Chen, J.; Derfler, B.; Maskati, A.
  • Proceedings of the National Academy of Sciences, Vol. 86, Issue 20
  • DOI: 10.1073/pnas.86.20.7961

Toxicity and repair of DNA adducts produced by the natural product yatakemycin
journal, July 2017

  • Mullins, Elwood A.; Shi, Rongxin; Eichman, Brandt F.
  • Nature Chemical Biology, Vol. 13, Issue 9
  • DOI: 10.1038/nchembio.2439

A Catalytic Role for C–H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD
journal, September 2016

  • Parsons, Zachary D.; Bland, Joshua M.; Mullins, Elwood A.
  • Journal of the American Chemical Society, Vol. 138, Issue 36
  • DOI: 10.1021/jacs.6b07399

Mechanisms for enzymatic cleavage of the N-glycosidic bond in DNA
journal, January 2014

  • Drohat, Alexander C.; Maiti, Atanu
  • Org. Biomol. Chem., Vol. 12, Issue 42
  • DOI: 10.1039/C4OB01063A

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Properties of 3-methyladenine-DNA glycosylase from Escherichia coli
journal, May 1978


Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli.
journal, March 1984


Three-dimensional structure of the Stat3β homodimer bound to DNA
journal, July 1998

  • Becker, Stefan; Groner, Bernd; Müller, Christoph W.
  • Nature, Vol. 394, Issue 6689
  • DOI: 10.1038/28101

Self-Resistance to an Antitumor Antibiotic: A DNA Glycosylase Triggers the Base-Excision Repair System in Yatakemycin Biosynthesis
journal, September 2012

  • Xu, Hui; Huang, Wei; He, Qing-Li
  • Angewandte Chemie International Edition, Vol. 51, Issue 42
  • DOI: 10.1002/anie.201204109

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
journal, January 2011

  • Sievers, Fabian; Wilm, Andreas; Dineen, David
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.75

Origins of Specificity in Protein-DNA Recognition
journal, June 2010


Nucleic acid recognition by tandem helical repeats
journal, February 2012

  • Rubinson, Emily H.; Eichman, Brandt F.
  • Current Opinion in Structural Biology, Vol. 22, Issue 1
  • DOI: 10.1016/j.sbi.2011.11.005

Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats
journal, March 2007

  • Dalhus, Bjørn; Helle, Ina Høydal; Backe, Paul H.
  • Nucleic Acids Research, Vol. 35, Issue 7
  • DOI: 10.1093/nar/gkm039

From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis
journal, April 2013

  • McAndrew, Ryan P.; Park, Joshua I.; Heins, Richard A.
  • Journal of Biological Chemistry, Vol. 288, Issue 21
  • DOI: 10.1074/jbc.M113.458356

Profiling base excision repair glycosylases with synthesized transition state analogs
journal, September 2011

  • Chu, Aurea M.; Fettinger, James C.; David, Sheila S.
  • Bioorganic & Medicinal Chemistry Letters, Vol. 21, Issue 17
  • DOI: 10.1016/j.bmcl.2011.05.085

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011

  • Letunic, I.; Bork, P.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr201

Methylating Agents and DNA Repair Responses:  Methylated Bases and Sources of Strand Breaks
journal, December 2006

  • Wyatt, Michael D.; Pittman, Douglas L.
  • Chemical Research in Toxicology, Vol. 19, Issue 12
  • DOI: 10.1021/tx060164e

Immunoglobulin domains in Escherichia coli and other enterobacteria: from pathogenesis to applications in antibody technologies
journal, March 2013


[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997


Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206