Evolutionary history and higher order classification of AAA+ ATPases.

[1]  Detlef D. Leipe,et al.  Evolution and classification of P-loop kinases and related proteins. , 2003, Journal of molecular biology.

[2]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[3]  J. Decaprio,et al.  Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen , 2003, Nature.

[4]  N. Grishin,et al.  Peptidase family U34 belongs to the superfamily of N‐terminal nucleophile hydrolases , 2003, Protein science : a publication of the Protein Society.

[5]  Craig M. Ogata,et al.  The structure and function of MCM from archaeal M. Thermoautotrophicum , 2003, Nature Structural Biology.

[6]  Z. Kelman,et al.  Structural lessons in DNA replication from the third domain of life , 2003, Nature Structural Biology.

[7]  Ronald D Vale,et al.  The Molecular Motor Toolbox for Intracellular Transport , 2003, Cell.

[8]  R. Giraldo Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. , 2003, FEMS microbiology reviews.

[9]  J. Dujardin,et al.  Eubacterial HslV and HslU subunits homologs in primordial eukaryotes. , 2002, Molecular biology and evolution.

[10]  L. Esser,et al.  Crystal Structure of ClpA, an Hsp100 Chaperone and Regulator of ClpAP Protease* , 2002, The Journal of Biological Chemistry.

[11]  W. Rottbauer,et al.  Reptin and Pontin Antagonistically Regulate Heart Growth in Zebrafish Embryos , 2002, Cell.

[12]  J. Kuriyan,et al.  Motors and switches: AAA+ machines within the replisome , 2002, Nature Reviews Molecular Cell Biology.

[13]  B. Bukau,et al.  AAA+ proteins and substrate recognition, it all depends on their partner in crime , 2002, FEBS letters.

[14]  Patrick Forterre,et al.  The origin of DNA genomes and DNA replication proteins. , 2002, Current opinion in microbiology.

[15]  R. Willows,et al.  Three semidominant barley mutants with single amino acid substitutions in the smallest magnesium chelatase subunit form defective AAA+ hexamers , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[16]  J. Berger,et al.  The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation , 2002, The EMBO journal.

[17]  Yusuke Nakamura,et al.  Isolation of HELAD1, a novel human helicase gene up-regulated in colorectal carcinomas , 2002, Oncogene.

[18]  H. Shinagawa,et al.  Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. , 2002, Molecular cell.

[19]  L. Aravind,et al.  Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome , 2002, Science.

[20]  M. Buck,et al.  Mechanochemical ATPases and transcriptional activation , 2002, Molecular microbiology.

[21]  Chandra Verma,et al.  The crystal structure of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli at 1.5 A resolution. , 2002, Structure.

[22]  Z. Kelman,et al.  The Methanobacterium thermoautotrophicum MCM protein can form heptameric rings , 2002, EMBO reports.

[23]  J. Vandekerckhove,et al.  unc-53 controls longitudinal migration in C. elegans. , 2002, Development.

[24]  I. Gibbons,et al.  Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein , 2002, BMC Genomics.

[25]  T. Fukui,et al.  A Membrane-Bound Archaeal Lon Protease Displays ATP-Independent Proteolytic Activity towards Unfolded Proteins and ATP-Dependent Activity for Folded Proteins , 2002, Journal of bacteriology.

[26]  M. O’Donnell,et al.  The DnaC helicase loader is a dual ATP/ADP switch protein , 2002, The EMBO journal.

[27]  T. Mizushima,et al.  The structure of the mammalian 20S proteasome at 2.75 A resolution. , 2002, Structure.

[28]  N. Cozzarelli,et al.  SV40 Large T Antigen Hexamer Structure Domain Organization and DNA-Induced Conformational Changes , 2002, Current Biology.

[29]  Detlef D. Leipe,et al.  Classification and evolution of P-loop GTPases and related ATPases. , 2002, Journal of molecular biology.

[30]  W. Donachie FtsK: Maxwell's Demon? , 2002, Molecular cell.

[31]  D. Sherratt,et al.  FtsK Is a DNA Motor Protein that Activates Chromosome Dimer Resolution by Switching the Catalytic State of the XerC and XerD Recombinases , 2002, Cell.

[32]  A. Lupas,et al.  Molecular evolution of proteasomes. , 2002, Current topics in microbiology and immunology.

[33]  E. Koonin,et al.  Common Origin of Four Diverse Families of Large Eukaryotic DNA Viruses , 2001, Journal of Virology.

[34]  Lesilee S. Rose,et al.  The Caenorhabditis elegans polarity gene ooc-5 encodes a Torsin-related protein of the AAA ATPase superfamily. , 2001, Development.

[35]  P. Grandi,et al.  Identification of a 60S preribosomal particle that is closely linked to nuclear export. , 2001, Molecular cell.

[36]  Kunihiro Matsumoto,et al.  Chl12 (Ctf18) Forms a Novel Replication Factor C-Related Complex and Functions Redundantly with Rad24 in the DNA Replication Checkpoint Pathway , 2001, Molecular and Cellular Biology.

[37]  J. Tainer,et al.  Structure and mechanism of the RuvB Holliday junction branch migration motor. , 2001, Journal of molecular biology.

[38]  J. Olsen,et al.  Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase. , 2001, Journal of molecular biology.

[39]  A. Wilkinson,et al.  AAA+ superfamily ATPases: common structure–diverse function , 2001, Genes to cells : devoted to molecular & cellular mechanisms.

[40]  S. Müller,et al.  The McrBC restriction endonuclease assembles into a ring structure in the presence of G nucleotides , 2001, The EMBO journal.

[41]  T. Masuko,et al.  A Novel Protein Interacts with the Werner's Syndrome Gene Product Physically and Functionally* , 2001, The Journal of Biological Chemistry.

[42]  E V Koonin,et al.  Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. , 2001, Journal of molecular biology.

[43]  E V Koonin,et al.  Apoptotic molecular machinery: vastly increased complexity in vertebrates revealed by genome comparisons. , 2001, Science.

[44]  G. Mocz,et al.  Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases. , 2001, Structure.

[45]  Fernando de la Cruz,et al.  The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase , 2001, Nature.

[46]  B. Sathyanarayana,et al.  Clp ATPases and their role in protein unfolding and degradation. , 2001, Advances in protein chemistry.

[47]  K. Fröhlich An AAA family tree. , 2001, Journal of cell science.

[48]  M. O’Donnell,et al.  Mechanisms of DNA replication. , 2000, Current opinion in chemical biology.

[49]  L. Bolund,et al.  Human and mouse mitochondrial orthologs of bacterial ClpX , 2000, Mammalian Genome.

[50]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[51]  J M Berger,et al.  Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control. , 2000, Molecular cell.

[52]  S. Bell,et al.  ATPase switches controlling DNA replication initiation. , 2000, Current opinion in cell biology.

[53]  Robert Huber,et al.  The structures of HslU and the ATP-dependent protease HslU–HslV , 2000, Nature.

[54]  M. Cole,et al.  An ATPase/helicase complex is an essential cofactor for oncogenic transformation by c-Myc. , 2000, Molecular cell.

[55]  B. Snel,et al.  Gene and context: integrative approaches to genome analysis. , 2000, Advances in protein chemistry.

[56]  Detlef D. Leipe,et al.  The bacterial replicative helicase DnaB evolved from a RecA duplication. , 2000, Genome research.

[57]  E V Koonin,et al.  Protein fold recognition using sequence profiles and its application in structural genomics. , 2000, Advances in protein chemistry.

[58]  P. Hanawalt,et al.  A phylogenomic study of DNA repair genes, proteins, and processes. , 1999, Mutation research.

[59]  E. Koonin,et al.  DNA-binding proteins and evolution of transcription regulation in the archaea. , 1999, Nucleic acids research.

[60]  Y. Igarashi,et al.  The cbbQ genes, located downstream of the form I and form II RubisCO genes, affect the activity of both RubisCOs. , 1999, Biochemical and biophysical research communications.

[61]  H. Kessler,et al.  The solution structure of VAT-N reveals a ‘missing link’ in the evolution of complex enzymes from a simple βαββ element , 1999, Current Biology.

[62]  R A Stuart,et al.  Bcs1p, an AAA‐family member, is a chaperone for the assembly of the cytochrome bc1 complex , 1999, The EMBO journal.

[63]  Nikos Kyrpides,et al.  Universal Protein Families and the Functional Content of the Last Universal Common Ancestor , 1999, Journal of Molecular Evolution.

[64]  A. Pingoud,et al.  The GTP-binding domain of McrB: more than just a variation on a common theme? , 1999, Journal of molecular biology.

[65]  Detlef D. Leipe,et al.  Did DNA replication evolve twice independently? , 1999, Nucleic acids research.

[66]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[67]  E. Koonin,et al.  Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. , 1999, Journal of molecular biology.

[68]  E. Koonin,et al.  Conserved domains in DNA repair proteins and evolution of repair systems. , 1999, Nucleic acids research.

[69]  Kenji Mizuguchi,et al.  A six-stranded double-psi β barrel is shared by several protein superfamilies , 1999 .

[70]  A. F. Neuwald The hexamerization domain of N-ethylmaleimide-sensitive factor: structural clues to chaperone function. , 1999, Structure.

[71]  I R Vetter,et al.  Nucleoside triphosphate-binding proteins: different scaffolds to achieve phosphoryl transfer , 1999, Quarterly Reviews of Biophysics.

[72]  E V Koonin,et al.  AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. , 1999, Genome research.

[73]  A EisenJ,et al.  DNA修復遺伝子,タンパクと過程のphylogenomic(系統発生的ゲノム)調査 , 1999 .

[74]  T. Tamura,et al.  A notable example of an evolutionary conserved gene: studies on a putative DNA helicase TIP49. , 1999, DNA sequence : the journal of DNA sequencing and mapping.

[75]  M. O’Donnell,et al.  ATP Binding to the Escherichia coli Clamp Loader Powers Opening of the Ring-shaped Clamp of DNA Polymerase III Holoenzyme* , 1998, The Journal of Biological Chemistry.

[76]  Y. Igarashi,et al.  The nirQ gene, which is required for denitrification of Pseudomonas aeruginosa, can activate the RubisCO from Pseudomonas hydrogenothermophila. , 1998, Biochimica et biophysica acta.

[77]  W. Weis,et al.  Crystal Structure of the Hexamerization Domain of N-ethylmaleimide–Sensitive Fusion Protein , 1998, Cell.

[78]  S. Kustu,et al.  The bacterial enhancer-binding protein NtrC as a molecular machine. , 1998, Cold Spring Harbor symposia on quantitative biology.

[79]  James R. Brown,et al.  Archaea and the prokaryote-to-eukaryote transition. , 1997, Microbiology and molecular biology reviews : MMBR.

[80]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[81]  M. Purugganan,et al.  The Evolution of the Conserved ATPase Domain (CAD): Reconstructing the History of an Ancient Protein Module , 1997, Journal of Molecular Evolution.

[82]  Andrej Sali,et al.  Crystal Structure of the δ′ Subunit of the Clamp-Loader Complex of E. coli DNA Polymerase III , 1997, Cell.

[83]  A. Beyer Sequence analysis of the AAA protein family , 1997, Protein science : a publication of the Protein Society.

[84]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[85]  W. Doolittle,et al.  Archaea and the Origin(s) of DNA Replication Proteins , 1997, Cell.

[86]  E V Koonin,et al.  Evidence for a Family of Archaeal ATPases , 1997, Science.

[87]  D. Markovitz,et al.  Bacterial Protease Lon Is a Site-specific DNA-binding Protein* , 1997, The Journal of Biological Chemistry.

[88]  M C Peitsch,et al.  ProMod and Swiss-Model: Internet-based tools for automated comparative protein modelling. , 1996, Biochemical Society transactions.

[89]  J. Felsenstein Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. , 1996, Methods in enzymology.

[90]  C. Sander,et al.  Dali: a network tool for protein structure comparison. , 1995, Trends in biochemical sciences.

[91]  F. Confalonieri,et al.  A 200‐amino acid ATPase module in search of a basic function , 1995, BioEssays : news and reviews in molecular, cellular and developmental biology.

[92]  H. Mori,et al.  Escherichia coli FtsH is a membrane‐bound, ATP‐dependent protease which degrades the heat‐shock transcription factor sigma 32. , 1995, The EMBO journal.

[93]  W Baumeister,et al.  Proteasome from Thermoplasma acidophilum: a threonine protease. , 1995, Science.

[94]  E. Egelman,et al.  Bacteriophage T7 helicase/primase proteins form rings around single-stranded DNA that suggest a general structure for hexameric helicases. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[95]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[96]  B. Rost,et al.  Combining evolutionary information and neural networks to predict protein secondary structure , 1994, Proteins.

[97]  Sudhir Kumar,et al.  MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers , 1994, Comput. Appl. Biosci..

[98]  E V Koonin,et al.  A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication. , 1993, Nucleic acids research.

[99]  R. Wickner,et al.  VYeast sequencing reports. AFG1, a new member of the SEC18–NSF, PAS1, CDC48–VCP, TBP family of ATPases , 1992, Yeast.

[100]  P Bork,et al.  An ATPase domain common to prokaryotic cell cycle proteins, sugar kinases, actin, and hsp70 heat shock proteins. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[101]  T. Steitz,et al.  Structure of the recA protein–ADP complex , 1992, Nature.

[102]  J. Adachi,et al.  MOLPHY, programs for molecular phylogenetics , 1992 .

[103]  R. V. van Spanning,et al.  Isolation and characterization of the moxJ, moxG, moxI, and moxR genes of Paracoccus denitrificans: inactivation of moxJ, moxG, and moxR and the resultant effect on methylotrophic growth , 1991, Journal of bacteriology.

[104]  J. Coggins,et al.  Evidence for an ancestral core structure in nucleotide-binding proteins with the type A motif. , 1991, Journal of molecular biology.

[105]  C. Englert,et al.  A DNA region of 9kbp contains all genes necessary for gas vesicle synthesis in halophilic archaebacteria , 1991, Molecular microbiology.

[106]  P. R. Sibbald,et al.  The P-loop--a common motif in ATP- and GTP-binding proteins. , 1990, Trends in biochemical sciences.

[107]  E. Koonin,et al.  A new superfamily of putative NTP‐binding domains encoded by genomes of small DNA and RNA viruses , 1990, FEBS letters.

[108]  E. Koonin,et al.  Viral proteins containing the purine NTP-binding sequence pattern. , 1989, Nucleic acids research.

[109]  J. Walker,et al.  Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold. , 1982, The EMBO journal.