A naturally chimeric type IIA topoisomerase in Aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs.

PubWeight™: 0.97‹?› | Rank: Top 15%

🔗 View Article (PMC 3009783)

Published in Proc Natl Acad Sci U S A on November 12, 2010

Authors

Elsa M Tretter1, Jeffrey C Lerman, James M Berger

Author Affiliations

1: Division of Biochemistry and Molecular Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

Articles citing this

All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol (2011) 2.66

Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency. J Biol Chem (2012) 1.01

Drug interactions with Bacillus anthracis topoisomerase IV: biochemical basis for quinolone action and resistance. Biochemistry (2011) 1.01

Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity. J Biol Chem (2012) 0.97

Guiding strand passage: DNA-induced movement of the gyrase C-terminal domains defines an early step in the supercoiling cycle. Nucleic Acids Res (2011) 0.89

Role of the water-metal ion bridge in mediating interactions between quinolones and Escherichia coli topoisomerase IV. Biochemistry (2014) 0.85

Chiral discrimination and writhe-dependent relaxation mechanism of human topoisomerase IIα. J Biol Chem (2013) 0.83

Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV. J Mol Biol (2013) 0.83

Bacillus anthracis GrlAV96A topoisomerase IV, a quinolone resistance mutation that does not affect the water-metal ion bridge. Antimicrob Agents Chemother (2014) 0.77

Evolutionary twist on topoisomerases: conversion of gyrase to topoisomerase IV. Proc Natl Acad Sci U S A (2010) 0.75

Investigating the Roles of the C-Terminal Domain of Plasmodium falciparum GyrA. PLoS One (2015) 0.75

The tail that wags the dog: topoisomerase IV ParC C-terminal domain controls strand passage activity through multipartite topology-dependent interactions with DNA. J Mol Biol (2013) 0.75

Articles cited by this

Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01

PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr (2002) 53.61

Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins (2003) 32.38

Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84

DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci U S A (1976) 17.42

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature (1998) 7.77

Multiple alignment of DNA sequences with MAFFT. Methods Mol Biol (2009) 7.59

New topoisomerase essential for chromosome segregation in E. coli. Cell (1990) 7.19

An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature (1997) 7.06

Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng (2001) 5.71

Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA. Proc Natl Acad Sci U S A (1978) 4.54

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys (2008) 3.50

Site-specific cleavage of DNA by E. coli DNA gyrase. Cell (1979) 3.45

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol (2010) 3.42

Cleavage of DNA by mammalian DNA topoisomerase II. J Biol Chem (1983) 3.05

Superhelical Escherichia coli DNA: relaxation by coumermycin. J Mol Biol (1978) 2.95

Double strand DNA cleavage by type II DNA topoisomerase from Drosophila melanogaster. J Biol Chem (1983) 2.69

Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem (2000) 2.58

Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc Natl Acad Sci U S A (2003) 2.15

The structural basis for substrate specificity in DNA topoisomerase IV. J Mol Biol (2005) 2.08

Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev (2000) 1.94

Origin and evolution of DNA topoisomerases. Biochimie (2007) 1.94

The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc Natl Acad Sci U S A (2004) 1.93

Decatenation activity of topoisomerase IV during oriC and pBR322 DNA replication in vitro. Proc Natl Acad Sci U S A (1993) 1.91

The C-terminal domain of the Escherichia coli DNA gyrase A subunit is a DNA-binding protein. Nucleic Acids Res (1991) 1.74

Conversion of DNA gyrase into a conventional type II topoisomerase. Proc Natl Acad Sci U S A (1996) 1.70

Evolution of protein function, from a structural perspective. Curr Opin Chem Biol (1999) 1.61

Bacterial diversity based on type II DNA topoisomerase genes. Annu Rev Genet (1996) 1.55

Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism. Biochem Soc Trans (2005) 1.55

The unique DNA topology and DNA topoisomerases of hyperthermophilic archaea. FEMS Microbiol Rev (1996) 1.48

Evolution of the beta-propeller fold. Proteins (2008) 1.48

Requirement of topoisomerase IV parC and parE genes for cell cycle progression and developmental regulation in Caulobacter crescentus. Mol Microbiol (1997) 1.46

A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem (2005) 1.41

Arabidopsis thaliana DNA gyrase is targeted to chloroplasts and mitochondria. Proc Natl Acad Sci U S A (2004) 1.32

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Res (2009) 1.25

Natural synthesis of a DNA-binding protein from the C-terminal domain of DNA gyrase A in Borrelia burgdorferi. EMBO J (1999) 1.15

Functional characterisation of mycobacterial DNA gyrase: an efficient decatenase. Nucleic Acids Res (2002) 1.13

The "GyrA-box" is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction. J Biol Chem (2005) 1.11

Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. J Biol Chem (2004) 1.07

Twisting of the DNA-binding surface by a beta-strand-bearing proline modulates DNA gyrase activity. Nucleic Acids Res (2010) 1.05

DNA gyrase from Thermotoga maritima. Methods Enzymol (2001) 0.77

Articles by these authors

Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Dev Cell (2005) 4.83

Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu Rev Biophys Biomol Struct (2006) 4.74

A robust and scalable microfluidic metering method that allows protein crystal growth by free interface diffusion. Proc Natl Acad Sci U S A (2002) 4.16

DNA topoisomerases: harnessing and constraining energy to govern chromosome topology. Q Rev Biophys (2008) 3.50

Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell (2009) 3.38

Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu Rev Biophys Biomol Struct (2004) 3.37

Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell (2003) 3.00

DNA replication initiation: mechanisms and regulation in bacteria. Nat Rev Microbiol (2007) 2.96

The structural basis for MCM2-7 helicase activation by GINS and Cdc45. Nat Struct Mol Biol (2011) 2.93

Structural basis for gate-DNA recognition and bending by type IIA topoisomerases. Nature (2007) 2.79

Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol (2006) 2.73

The protective antigen component of anthrax toxin forms functional octameric complexes. J Mol Biol (2009) 2.69

All tangled up: how cells direct, manage and exploit topoisomerase function. Nat Rev Mol Cell Biol (2011) 2.66

Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export. Nat Cell Biol (2006) 2.58

Identification, function and structure of the mycobacterial sulfotransferase that initiates sulfolipid-1 biosynthesis. Nat Struct Mol Biol (2004) 2.25

Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. Science (2007) 2.10

The structural basis for substrate specificity in DNA topoisomerase IV. J Mol Biol (2005) 2.08

Structure and function of the conserved core of histone deposition protein Asf1. Curr Biol (2003) 2.02

The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation. EMBO J (2002) 1.98

Structure of human cGAS reveals a conserved family of second-messenger enzymes in innate immunity. Cell Rep (2013) 1.96

The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc Natl Acad Sci U S A (2004) 1.93

The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes Dev (2004) 1.90

The structure of DNA-bound human topoisomerase II alpha: conformational mechanisms for coordinating inter-subunit interactions with DNA cleavage. J Mol Biol (2012) 1.87

Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. Nat Struct Mol Biol (2006) 1.80

Identification of residues in yeast Spo11p critical for meiotic DNA double-strand break formation. Mol Cell Biol (2002) 1.77

Suite of three protein crystallography beamlines with single superconducting bend magnet as the source. J Synchrotron Radiat (2004) 1.70

A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature (2011) 1.70

A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination. J Am Chem Soc (2006) 1.65

Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure (2012) 1.64

The N-terminal domain of Nup159 forms a beta-propeller that functions in mRNA export by tethering the helicase Dbp5 to the nuclear pore. Mol Cell (2004) 1.59

A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases. Nature (2010) 1.59

Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell (2006) 1.58

Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol Cell (2005) 1.57

DNA stretching by bacterial initiators promotes replication origin opening. Nature (2011) 1.55

Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators. Cell (2008) 1.51

Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187. Proc Natl Acad Sci U S A (2003) 1.44

The nuts and bolts of ring-translocase structure and mechanism. Curr Opin Struct Biol (2011) 1.44

Identification of a DNA primase template tracking site redefines the geometry of primer synthesis. Nat Struct Mol Biol (2008) 1.42

Escherichia coli condensin MukB stimulates topoisomerase IV activity by a direct physical interaction. Proc Natl Acad Sci U S A (2010) 1.41

Function and structure of a prokaryotic formylglycine-generating enzyme. J Biol Chem (2008) 1.35

Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics. BMC Struct Biol (2006) 1.34

Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D. J Biol Chem (2006) 1.31

AAA+ ATPases in the initiation of DNA replication. Crit Rev Biochem Mol Biol (2008) 1.29

Mechanisms for initiating cellular DNA replication. Annu Rev Biochem (2013) 1.28

THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat Struct Mol Biol (2009) 1.27

The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins. EMBO J (2005) 1.24

ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote. Proc Natl Acad Sci U S A (2012) 1.21

Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution. EMBO J (2003) 1.18

Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface. J Biol Chem (2006) 1.16

The bacterial DnaC helicase loader is a DnaB ring breaker. Cell (2013) 1.14

Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions. Nucleic Acids Res (2006) 1.13

Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2. Protein Sci (2007) 1.11

Origin remodeling and opening in bacteria rely on distinct assembly states of the DnaA initiator. J Biol Chem (2010) 1.10

A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Res (2010) 1.09

Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity. Nat Struct Mol Biol (2012) 1.09

Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding. J Biol Chem (2014) 1.08

Biochemical characterization of Cdc6/Orc1 binding to the replication origin of the euryarchaeon Methanothermobacter thermoautotrophicus. Nucleic Acids Res (2004) 1.08

Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases. Mol Microbiol (2008) 1.07

Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Mol Cell (2006) 1.07

The ancestral role of ATP hydrolysis in type II topoisomerases: prevention of DNA double-strand breaks. Nucleic Acids Res (2011) 1.07

Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI. Structure (2005) 1.06

A structural framework for replication origin opening by AAA+ initiation factors. Curr Opin Struct Biol (2012) 1.06

Asf1-like structure of the conserved Yaf9 YEATS domain and role in H2A.Z deposition and acetylation. Proc Natl Acad Sci U S A (2009) 1.05

Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface. J Mol Biol (2008) 1.03

Crystal structure of the DNA gyrase GyrA N-terminal domain from Mycobacterium tuberculosis. Proteins (2010) 1.03

Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI. Nat Struct Mol Biol (2007) 1.02

Mechanisms for defining supercoiling set point of DNA gyrase orthologs: II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole determinant for controlling supercoiling efficiency. J Biol Chem (2012) 1.01

Contributions of folding cores to the thermostabilities of two ribonucleases H. Protein Sci (2002) 0.99

The role of DNA bending in type IIA topoisomerase function. Nucleic Acids Res (2013) 0.98

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. J Mol Biol (2008) 0.98

Molecular determinants of origin discrimination by Orc1 initiators in archaea. Nucleic Acids Res (2011) 0.98

Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I. A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase activity. J Biol Chem (2012) 0.97

ATP binding controls distinct structural transitions of Escherichia coli DNA gyrase in complex with DNA. Nat Struct Mol Biol (2012) 0.97

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure (2005) 0.97

The crystal structure of the hinge domain of the Escherichia coli structural maintenance of chromosomes protein MukB. J Mol Biol (2009) 0.97

Macro-to-micro structural proteomics: native source proteins for high-throughput crystallization. PLoS One (2012) 0.96

Structural and biochemical characterization of the interaction between KPC-2 beta-lactamase and beta-lactamase inhibitor protein. Biochemistry (2009) 0.96

SnapShot: nucleic acid helicases and translocases. Cell (2008) 0.92

Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1. Proc Natl Acad Sci U S A (2009) 0.92

Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing. Proc Natl Acad Sci U S A (2011) 0.92

Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase. Biochemistry (2004) 0.91

Nanoscale protein assemblies from a circular permutant of the tobacco mosaic virus. Nano Lett (2010) 0.89

Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A. Protein Sci (2005) 0.89

Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug radicicol. Nucleic Acids Res (2006) 0.88

Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo. EMBO J (2013) 0.87

FASTDXL: a generalized screen to trap disulfide-stabilized complexes for use in structural studies. Structure (2007) 0.87

Structure of the ATP-binding domain of Plasmodium falciparum Hsp90. Proteins (2010) 0.87

Emerging roles for plant topoisomerase VI. Chem Biol (2003) 0.86

Unraveling the early steps of prokaryotic replication. Curr Opin Struct Biol (2005) 0.83

A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. Elife (2013) 0.83

Bypassing fluoroquinolone resistance with quinazolinediones: studies of drug-gyrase-DNA complexes having implications for drug design. ACS Chem Biol (2014) 0.83

Hyperthermophilic Aquifex aeolicus initiates primer synthesis on a limited set of trinucleotides comprised of cytosines and guanines. Nucleic Acids Res (2008) 0.83

Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV. J Mol Biol (2013) 0.83

Real-time detection of DNA topological changes with a fluorescently labeled cruciform. Nucleic Acids Res (2013) 0.81

Crystallization and X-ray structure determination of an RNA-dependent hexameric helicase. Methods Enzymol (2012) 0.79

False memory syndrome and therapist liability to third parties for emotional distress injuries arising from recovered memory therapy: a general prohibition on liability and a limited liability exception. Spec Law Dig Health Care Law (2002) 0.76