Noncanonical prokaryotic X family DNA polymerases lack polymerase activity and act as exonucleases

The PHP domain of PolX from Staphylococcus aureus aids high fidelity DNA synthesis through the removal of misincorporated deoxyribo-, ribo- and oxidized nucleotides

(2021) Shilpi Nagpal et al.   Scientific Reports

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Molecular and structural characterization of oxidized ribonucleotide insertion into DNA by human DNA polymerase β

(2020) Mallory R. Smith et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The In Vitro Non-Tetramerizing ZapAI83E Mutant Is Unable to Recruit ZapB to the Division Plane In Vivo in Escherichia coli

(2020) Nils Y. Meiresonne et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PDBMD2CD: providing predicted protein circular dichroism spectra from multiple molecular dynamics-generated protein structures

(2020) Elliot D Drew et al.   NUCLEIC ACIDS RESEARCH

Evolutionary and Comparative analysis of bacterial Non-Homologous End Joining Repair

(2020) Mohak Sharda et al.   Genome Biology and Evolution

Assembly properties of bacterial tubulin homolog FtsZ regulated by the positive regulator protein ZipA and ZapA from Pseudomonas aeruginosa

(2020) Mujeeb ur Rahman et al.   Scientific Reports

An updated structural classification of replicative DNA polymerases

(2019) Pierre Raia et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Bacillus subtilis MutS Modulates RecA-Mediated DNA Strand Exchange Between Divergent DNA Sequences

(2019) Begoña Carrasco et al.   Frontiers in Microbiology

New insights into the structures and interactions of bacterial Y-family DNA polymerases

(2019) Kęstutis Timinskas et al.   NUCLEIC ACIDS RESEARCH

Bacterial NHEJ: a never ending story

(2019) Claire Bertrand et al.   MOLECULAR MICROBIOLOGY

Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions

(2019) Yao-Kai Chang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An array of basic residues is essential for the nucleolytic activity of the PHP domain of bacterial/archaeal PolX DNA polymerases

(2019) Guillermo Rodríguez et al.   Scientific Reports

Structure and function relationships in mammalian DNA polymerases

(2019) Nicole M. Hoitsma et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism

(2018) Wei Yang et al.   Annual Review of Biochemistry

Study of the Lyase Activity of Human DNA Polymerase β Using Analogues of the Intermediate Schiff Base Complex

(2018) Sasha M. Daskalova et al.   BIOCHEMISTRY

Eukaryotic DNA polymerases

(2018) Rinku Jain et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

(2017) Nicholas R. Pannunzio et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Non-homologous DNA end joining and alternative pathways to double-strand break repair

(2017) Howard H. Y. Chang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MutS2 Promotes Homologous Recombination in Bacillus subtilis

(2016) Peter E. Burby et al.   JOURNAL OF BACTERIOLOGY

Structural Mechanism for the Fidelity Modulation of DNA Polymerase λ

(2016) Mu-Sen Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader

(2015) Jeremy M Rock et al.   NATURE GENETICS

Structure–Function Studies of DNA Polymerase λ

(2014) Katarzyna Bebenek et al.   BIOCHEMISTRY

Structure and Mechanism of DNA Polymerase β

(2014) William A. Beard et al.   BIOCHEMISTRY

Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members

(2014) Rachelle J. Bienstock et al.   DNA REPAIR

Error-Prone Processing of Apurinic/Apyrimidinic (AP) Sites by PolX Underlies a Novel Mechanism That Promotes Adaptive Mutagenesis in Bacillus subtilis

(2014) R. d. C. Barajas-Ornelas et al.   JOURNAL OF BACTERIOLOGY

How a Low-Fidelity DNA Polymerase Chooses Non-Watson–Crick from Watson–Crick Incorporation

(2014) Wen-Jin Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origins of major archaeal clades correspond to gene acquisitions from bacteria

(2014) Shijulal Nelson-Sathi et al.   NATURE

Phylogenomic clustering for selecting non-redundant genomes for comparative genomics

(2013) G. Moreno-Hagelsieb et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The active site of TthPolX is adapted to prevent 8-oxo-dGTP misincorporation

(2013) Patricia Garrido et al.   NUCLEIC ACIDS RESEARCH

The Minimal Bacillus subtilis Nonhomologous End Joining Repair Machinery

(2013) Miguel de Vega   PLoS One

The role of the PHP domain associated with DNA polymerase X from Thermus thermophilus HB8 in base excision repair

(2012) Shuhei Nakane et al.   DNA REPAIR

A MatP-divisome interaction coordinates chromosome segregation with cell division inE. coli

(2012) Olivier Espéli et al.   EMBO JOURNAL

The Structural Basis of the Kinetic Mechanism of a Gap-Filling X-Family DNA Polymerase That Binds Mg2+-dNTP Before Binding to DNA

(2012) Shuhei Nakane et al.   JOURNAL OF MOLECULAR BIOLOGY

Microhomology-mediated DNA strand annealing and elongation by human DNA polymerases λ and β on normal and repetitive DNA sequences

(2012) Emmanuele Crespan et al.   NUCLEIC ACIDS RESEARCH

DNA Replicases from a Bacterial Perspective

(2011) Charles S. McHenry   Annual Review of Biochemistry

Characterization of marine X-family DNA polymerases and comparative analysis of base excision repair proteins

(2011) Hirofumi Kodera et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Molecular Insights into DNA Polymerase Deterrents for Ribonucleotide Insertion

(2011) Nisha A. Cavanaugh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Essential roles for imuA'- and imuB-encoded accessory factors in DnaE2-dependent mutagenesis in Mycobacterium tuberculosis

(2010) D. F. Warner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites

(2010) B. Banos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA polymerase Family X: Function, structure, and cellular roles

(2009) Jennifer Yamtich et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Family X DNA Polymerase fromDeinococcus radioduransAdopts a Non-standard Extended Conformation

(2009) Nicolas Leulliot et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Novel Mechanism of Sugar Selection Utilized by a Human X-Family DNA Polymerase

(2009) Jessica A. Brown et al.   JOURNAL OF MOLECULAR BIOLOGY

DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase

(2009) N. P. Khairnar et al.   MICROBIOLOGY-SGM

Characterization of DNA polymerase X from Thermus thermophilus HB8 reveals the POLXc and PHP domains are both required for 3′–5′ exonuclease activity

(2009) Shuhei Nakane et al.   NUCLEIC ACIDS RESEARCH

Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in human

(2009) Krzysztof Kuchta et al.   NUCLEIC ACIDS RESEARCH

Altered Order of Substrate Binding by DNA Polymerase X from African Swine Fever Virus†

(2008) Sandeep Kumar et al.   BIOCHEMISTRY

Distribution and roles of X-family DNA polymerases in eukaryotes

(2008) Yukinobu Uchiyama et al.   BIOCHIMIE

A comparison of BRCT domains involved in nonhomologous end-joining: Introducing the solution structure of the BRCT domain of polymerase lambda

(2008) Geoffrey A. Mueller et al.   DNA REPAIR

Insights into the Replisome from the Structure of a Ternary Complex of the DNA Polymerase III α-Subunit

(2008) Richard A. Wing et al.   JOURNAL OF MOLECULAR BIOLOGY

Editing of misaligned 3'-termini by an intrinsic 3'-5' exonuclease activity residing in the PHP domain of a family X DNA polymerase

(2008) B. Banos et al.   NUCLEIC ACIDS RESEARCH