Comprehensive classification of the PIN domain-like superfamily

The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans

(2016) Graeme R. Wells et al.   NUCLEIC ACIDS RESEARCH

RNA damage in biological conflicts and the diversity of responding RNA repair systems

(2016) A. Maxwell Burroughs et al.   NUCLEIC ACIDS RESEARCH

Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors

(2016) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

VapCs of Mycobacterium tuberculosis cleave RNAs essential for translation

(2016) Kristoffer Winther et al.   NUCLEIC ACIDS RESEARCH

Two NYN domain containing putative nucleases are involved in transcript maturation in Arabidopsis mitochondria

(2016) Birgit Stoll et al.   PLANT JOURNAL

Differential substrate recognition by isozymes of plant protein-only Ribonuclease P

(2016) Michael J. Howard et al.   RNA

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions

(2016) Mariko Yokogawa et al.   Scientific Reports

Cellular 5′-3′ mRNA Exonuclease Xrn1 Controls Double-Stranded RNA Accumulation and Anti-Viral Responses

(2015) Hannah M. Burgess et al.   Cell Host & Microbe

Domain characterization ofBacillus subtilisGabR, a pyridoxal 5′-phosphate-dependent transcriptional regulator

(2015) Keita Okuda et al.   JOURNAL OF BIOCHEMISTRY

Mechanistic Studies Reveal Similar Catalytic Strategies for Phosphodiester Bond Hydrolysis by Protein-only and RNA-dependent Ribonuclease P

(2015) Michael J. Howard et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dissecting the Roles of the 5′ Exoribonucleases Xrn1 and Xrn2 in Restricting Hepatitis C Virus Replication

(2015) You Li et al.   JOURNAL OF VIROLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The mycobacterial PhoH2 proteins are type II toxin antitoxins coupled to RNA helicase domains

(2015) Emma S.V. Andrews et al.   TUBERCULOSIS

Growth-regulating Mycobacterium tuberculosis VapC-mt4 toxin is an isoacceptor-specific tRNase

(2015) Jonathan W. Cruz et al.   Nature Communications

tRNAs taking charge

(2015) Jonathan W. Cruz et al.   Pathogens and Disease

A Proteome-Scale Map of the Human Interactome Network

(2014) Thomas Rolland et al.   CELL

Crystal structure of the VapBC-15 complex from Mycobacterium tuberculosis reveals a two-metal ion dependent PIN-domain ribonuclease and a variable mode of toxin–antitoxin assembly

(2014) Uddipan Das et al.   JOURNAL OF STRUCTURAL BIOLOGY

Radiation response inDeinococcus deserti: IrrE is a metalloprotease that cleaves repressor protein DdrO

(2014) Monika Ludanyi et al.   MOLECULAR MICROBIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

PubServer: literature searches by homology

(2014) Lukasz Jaroszewski et al.   NUCLEIC ACIDS RESEARCH

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification

(2014) Karolina A. Majorek et al.   NUCLEIC ACIDS RESEARCH

Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells

(2014) Skye A. Schmidt et al.   NUCLEIC ACIDS RESEARCH

LMKB/MARF1 Localizes to mRNA Processing Bodies, Interacts with Ge-1, and Regulates IFI44L Gene Expression

(2014) Donald B. Bloch et al.   PLoS One

Analysis of Non-Typeable Haemophilous influenzae VapC1 Mutations Reveals Structural Features Required for Toxicity and Flexibility in the Active Site

(2014) Brooke Hamilton et al.   PLoS One

XRN 5′→3′ exoribonucleases: Structure, mechanisms and functions

(2013) Vinay K. Nagarajan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Identification and Characterization of Type II Toxin-Antitoxin Systems in the Opportunistic Pathogen Acinetobacter baumannii

(2013) M. Jurenaite et al.   JOURNAL OF BACTERIOLOGY

Zinc Finger Protein 451 Is a Novel Smad Corepressor in Transforming Growth Factor-β Signaling

(2013) Yili Feng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Global Analysis of Eukaryotic mRNA Degradation Reveals Xrn1-Dependent Buffering of Transcript Levels

(2013) Mai Sun et al.   MOLECULAR CELL

Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex

(2013) Debora Lika Makino et al.   NATURE

MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation

(2013) Ren-Jye Lin et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics of defense systems in archaea and bacteria

(2013) Kira S. Makarova et al.   NUCLEIC ACIDS RESEARCH

The structure of Escherichia coli ExoIX—implications for DNA binding and catalysis in flap endonucleases

(2013) Christopher S. Anstey-Gilbert et al.   NUCLEIC ACIDS RESEARCH

Computational identification of novel biochemical systems involved in oxidation, glycosylation and other complex modifications of bases in DNA

(2013) Lakshminarayan M. Iyer et al.   NUCLEIC ACIDS RESEARCH

To be or not to be: regulation of restriction–modification systems and other toxin–antitoxin systems

(2013) Iwona Mruk et al.   NUCLEIC ACIDS RESEARCH

Structural and functional analysis of Utp23, a yeast ribosome synthesis factor with degenerate PIN domain

(2013) J. Lu et al.   RNA

Human GEN1 and the SLX4-Associated Nucleases MUS81 and SLX1 Are Essential for the Resolution of Replication-Induced Holliday Junctions

(2013) Elizabeth Garner et al.   Cell Reports

Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

(2012) Kira S Makarova et al.   Biology Direct

Overexpression oflalA, a paralog oflabA, is capable of affecting both circadian gene expression and cell growth in the cyanobacteriumSynechococcus elongatusPCC 7942

(2012) Yasuhito Taniguchi et al.   FEBS LETTERS

A VapBC Toxin-Antitoxin Module Is a Posttranscriptional Regulator of Metabolic Flux in Mycobacteria

(2012) J. L. McKenzie et al.   JOURNAL OF BACTERIOLOGY

Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase

(2012) J. Xu et al.   NUCLEIC ACIDS RESEARCH

Flap endonucleases pass 5′-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5′-ends

(2012) Nikesh Patel et al.   NUCLEIC ACIDS RESEARCH

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

(2012) Kamil Steczkiewicz et al.   NUCLEIC ACIDS RESEARCH

A Novel Role of the PrpR as a Transcription Factor Involved in the Regulation of Methylcitrate Pathway in Mycobacterium tuberculosis

(2012) Paweł Masiewicz et al.   PLoS One

Meiosis arrest female 1 (MARF1) has nuage-like function in mammalian oocytes

(2012) Y.-Q. Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing

(2012) M. J. Howard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural basis for TetM-mediated tetracycline resistance

(2012) A. Donhofer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Determination of ribonuclease sequence-specificity using Pentaprobes and mass spectrometry

(2012) J. L. McKenzie et al.   RNA

The 5′ → 3′ exoribonuclease XRN1/Pacman and its functions in cellular processes and development

(2012) Christopher Iain Jones et al.   Wiley Interdisciplinary Reviews-RNA

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily

(2011) Susan E. Tsutakawa et al.   CELL

Structures of Human Exonuclease 1 DNA Complexes Suggest a Unified Mechanism for Nuclease Family

(2011) Jillian Orans et al.   CELL

Neutralizing Mutations of Carboxylates That Bind Metal 2 in T5 Flap Endonuclease Result in an Enzyme That Still Requires Two Metal Ions

(2011) Christopher G. Tomlinson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Crystal Structure of the VapBC Toxin–Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly

(2011) Christian Dienemann et al.   JOURNAL OF MOLECULAR BIOLOGY

Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations

(2011) Edina Rosta et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MCPIP1 Ribonuclease Antagonizes Dicer and Terminates MicroRNA Biogenesis through Precursor MicroRNA Degradation

(2011) Hiroshi I. Suzuki et al.   MOLECULAR CELL

Coupled 5′ Nucleotide Recognition and Processivity in Xrn1-Mediated mRNA Decay

(2011) Martin Jinek et al.   MOLECULAR CELL

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Structural and functional analysis of the archaeal endonuclease Nob1

(2011) Thomas Veith et al.   NUCLEIC ACIDS RESEARCH

Effect of Rickettsial Toxin VapC on Its Eukaryotic Host

(2011) Gilles Audoly et al.   PLoS One

Discovery and characterization of a unique mycobacterial heme acquisition system

(2011) M. V. Tullius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA

(2011) K. S. Winther et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unpairing and gating: sequence-independent substrate recognition by FEN superfamily nucleases

(2011) Jane A. Grasby et al.   TRENDS IN BIOCHEMICAL SCIENCES

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c

(2010) Garry W. Buchko et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Substrate recognition and catalysis by flap endonucleases and related enzymes

(2010) Christopher G. Tomlinson et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

OST-HTH: a novel predicted RNA-binding domain

(2010) Vivek Anantharaman et al.   Biology Direct

Dynamics of Cullin-RING Ubiquitin Ligase Network Revealed by Systematic Quantitative Proteomics

(2010) Eric J. Bennett et al.   CELL

The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L

(2010) Rafal Tomecki et al.   EMBO JOURNAL

Mechanism of Holliday junction resolution by the human GEN1 protein

(2010) U. Rass et al.   GENES & DEVELOPMENT

One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies

(2010) Cynthia M. Dupureur   Metallomics

A single Arabidopsis organellar protein has RNase P activity

(2010) Anthony Gobert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ODB: a database for operon organizations, 2011 update

(2010) S. Okuda et al.   NUCLEIC ACIDS RESEARCH

The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array

(2010) V. L. Arcus et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Nucleases: diversity of structure, function and mechanism

(2010) Wei Yang   QUARTERLY REVIEWS OF BIOPHYSICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A novel nicotine catabolic plasmid pMH1 in Pseudomonas sp. strain HF-1

(2009) Meizhen Wang et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Interleukin-1-inducible MCPIP protein has structural and functional properties of RNase and participates in degradation of IL-1β mRNA

(2009) Danuta Mizgalska et al.   FEBS Journal

Requirement for the ERI/DICER Complex in Endogenous RNA Interference and Sperm Development in Caenorhabditis elegans

(2009) Derek M. Pavelec et al.   GENETICS

A single-base resolution map of an archaeal transcriptome

(2009) O. Wurtzel et al.   GENOME RESEARCH

Crystal Structure of the IrrE Protein, a Central Regulator of DNA Damage Repair in Deinococcaceae

(2009) Andreja Vujičić-Žagar et al.   JOURNAL OF MOLECULAR BIOLOGY

CGIN1: A Retroviral Contribution to Mammalian Genomes

(2009) A. Marco et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ectopic production of VapCs fromEnterobacteriainhibits translation andtrans-activates YoeB mRNA interferase

(2009) Kristoffer S. Winther et al.   MOLECULAR MICROBIOLOGY

Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay

(2009) Kazufumi Matsushita et al.   NATURE

The Listeria transcriptional landscape from saprophytism to virulence

(2009) Alejandro Toledo-Arana et al.   NATURE

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

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

(2009) Krzysztof Kuchta et al.   NUCLEIC ACIDS RESEARCH

Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain

(2009) A. C. Lamanna et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicted poxvirus FEN1-like nuclease required for homologous recombination, double-strand break repair and full-size genome formation

(2009) T. G. Senkevich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Novel Gene, Encoding 6-Hydroxy-3-Succinoylpyridine Hydroxylase, Involved in Nicotine Degradation by Pseudomonas putida Strain S16

(2008) H. Tang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Active site substitutions delineate distinct classes of eubacterial flap endonuclease

(2008) Lee M. Allen et al.   BIOCHEMICAL JOURNAL

RNase P without RNA: Identification and Functional Reconstitution of the Human Mitochondrial tRNA Processing Enzyme

(2008) Johann Holzmann et al.   CELL

Roles of metal ions in nucleases

(2008) Cynthia M Dupureur   CURRENT OPINION IN CHEMICAL BIOLOGY

Three Metal Ions Participate in the Reaction Catalyzed by T5 Flap Endonuclease

(2008) Karl Syson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure and Proposed Activity of a Member of the VapBC Family of Toxin-Antitoxin Systems

(2008) Linda Miallau et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mini-III, an unusual member of the RNase III family of enzymes, catalyses 23S ribosomal RNA maturation in B. subtilis

(2008) Yulia Redko et al.   MOLECULAR MICROBIOLOGY

A conserved anti-repressor controls horizontal gene transfer by proteolysis

(2008) Baundauna Bose et al.   MOLECULAR MICROBIOLOGY

Endonucleolytic RNA cleavage by a eukaryotic exosome

(2008) Alice Lebreton et al.   NATURE

Identification of Holliday junction resolvases from humans and yeast

(2008) Stephen C. Y. Ip et al.   NATURE

SMG6 promotes endonucleolytic cleavage of nonsense mRNA in human cells

(2008) Andrea B Eberle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities

(2008) Daneen Schaeffer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2008) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of PAE0151 fromPyrobaculum aerophilum, a PIN-domain (VapC) protein from a toxin-antitoxin operon

(2008) Richard D. Bunker et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SMG6 is the catalytic endonuclease that cleaves mRNAs containing nonsense codons in metazoan

(2008) E. Huntzinger et al.   RNA