Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives.

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Common domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives. is …
instance of (P31):
scholarly articleQ13442814
review articleQ7318358

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P356DOI10.1111/J.1574-6976.2003.TB00629.X
P698PubMed publication ID12586394
P5875ResearchGate publication ID8221955

P50authorRafael GiraldoQ38319229
P2093author name stringRafael Giraldo
P2860cites workOrc6 involved in DNA replication, chromosome segregation, and cytokinesis.Q34143699
Geminivirus DNA replicationQ34158717
Bacterial replication initiator DnaA. Rules for DnaA binding and roles of DnaA in origin unwinding and helicase loadingQ34187344
Composing lifeQ34188557
Limiting DNA replication to once and only onceQ34192182
Understanding the enzymology of archaeal DNA replication: progress in form and functionQ34255371
Feedback controls restrain the initiation of Escherichia coli chromosomal replication.Q34308964
Translation: in retrospect and prospectQ34332282
Tubulin and FtsZ form a distinct family of GTPasesQ34471922
Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA bindingQ34488663
Eukaryotic transcription factorsQ34525919
Archaeal DNA replication: spotlight on a rapidly moving fieldQ34552203
Did DNA replication evolve twice independently?Q34707188
Automated detection of remote homologyQ34749949
Dynamic remodeling of transcription complexes by molecular chaperonesQ34784636
The Cdc6p nucleotide-binding motif is required for loading mcm proteins onto chromatinQ34812174
The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replicationQ34987457
The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooksQ35058094
Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP.Q35190125
Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor).Q35200597
Translocation pathway of protein substrates in ClpAP protease.Q35243928
Similarities between the DNA replication initiators of Gram-negative bacteria plasmids (RepA) and eukaryotes (Orc4p)/archaea (Cdc6p)Q35857244
A molecular chaperone, ClpA, functions like DnaK and DnaJ.Q35968116
The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6pQ22008054
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and EucaryaQ22066209
The antiquity of RNA-based evolutionQ22122345
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis toolsQ24248165
Functional organization of the yeast proteome by systematic analysis of protein complexesQ24292209
Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replicationQ24293201
A DNA helicase activity is associated with an MCM4, -6, and -7 protein complexQ24313590
Comparative genomics and evolution of proteins involved in RNA metabolismQ24515041
On the evolution of cellsQ24530769
DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin, oriC.Q24532816
The structure of a replication initiator unites diverse aspects of nucleic acid metabolismQ24533482
Making sense of eukaryotic DNA replication originsQ24535692
Origin pairing ('handcuffing') as a mode of negative control of P1 plasmid copy numberQ24536080
Processive DNA helicase activity of the minichromosome maintenance proteins 4, 6, and 7 complex requires forked DNA structuresQ24545600
Binding of cyclin-dependent kinases to ORC and Cdc6p regulates the chromosome replication cycleQ24555189
Evolution of the first metabolic cyclesQ24559932
The origin recognition complex interacts with a bipartite DNA binding site within yeast replicatorsQ24563569
Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DPQ24606785
Horizontal gene transfer among genomes: the complexity hypothesisQ24651300
Site-specific DNA binding of the Schizosaccharomyces pombe origin recognition complex is determined by the Orc4 subunitQ34012854
Polymerases and the replisome: machines within machines.Q34065994
About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisalQ34078677
Human origin recognition complex binds to the region of the latent origin of DNA replication of Epstein-Barr virusQ34081126
Cdc6 cooperates with Sic1 and Hct1 to inactivate mitotic cyclin-dependent kinases.Q34084309
Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coliQ34085669
The origin of cellular lifeQ34085683
The rotary mechanism of ATP synthaseQ34103409
Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45.Q34115837
The universal ancestorQ24655363
Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replicationQ24685710
Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 Å resolutionQ27619547
Structure of the winged-helix protein hRFX1 reveals a new mode of DNA bindingQ27621683
Structure of the 30S ribosomal subunitQ27627261
Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint controlQ27627450
Crystal structure of a DNA-dependent RNA polymerase (DNA primase)Q27629111
Structure and mechanism of the RuvB Holliday junction branch migration motorQ27633740
Prokaryotic origin of the actin cytoskeletonQ27634702
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIUQ27636245
Crystal structures of two intermediates in the assembly of the papillomavirus replication initiation complexQ27638318
Phage P4 origin-binding domain structure reveals a mechanism for regulation of DNA-binding activity by homo- and heterodimerization of winged helix proteinsQ27638712
Conserved structure for single-stranded telomeric DNA recognitionQ27638743
Structure and function of the BAH-containing domain of Orc1p in epigenetic silencingQ27639534
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiationQ27639653
Crystal structure of trp repressor/operator complex at atomic resolutionQ27728594
The B2 element of the Saccharomyces cerevisiae ARS1 origin of replication requires specific sequences to facilitate pre-RC formationQ27929960
Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phaseQ27930849
Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complexQ27931631
Formation of a preinitiation complex by S-phase cyclin CDK-dependent loading of Cdc45p onto chromatinQ27933399
Cdc6p-dependent loading of Mcm proteins onto pre-replicative chromatin in budding yeastQ27936236
The DNA replication fork in eukaryotic cells.Q27939216
Interdependent nuclear accumulation of budding yeast Cdt1 and Mcm2-7 during G1 phase.Q27940280
MCM proteins in DNA replicationQ27976474
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexesQ28131706
DNA replication in eukaryotic cellsQ28131747
Origin of life. Life as we don't know itQ28138162
The Cdt1 protein is required to license DNA for replication in fission yeastQ28141890
Subsets of human origin recognition complex (ORC) subunits are expressed in non-proliferating cells and associate with non-ORC proteinsQ28144369
Assembly of the human origin recognition complexQ28185696
Architecture of the human origin recognition complexQ28200779
Domain combinations in archaeal, eubacterial and eukaryotic proteomesQ28203959
Cyclin-dependent kinases prevent DNA re-replication through multiple mechanismsQ28204020
Insights into DNA replication from the third domain of lifeQ36095530
Heat shock proteins DnaJ, DnaK, and GrpE stimulate P1 plasmid replication by promoting initiator binding to the originQ36101720
Identification and reconstitution of the origin recognition complex from Schizosaccharomyces pombeQ36538083
Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscopeQ36770059
The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activityQ36774428
The replication initiation protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperoneQ36815340
A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicaseQ37107587
DnaJ, DnaK, and GrpE heat shock proteins are required in oriP1 DNA replication solely at the RepA monomerization stepQ37276537
Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication originQ37590548
A nucleotide switch in the Escherichia coli DnaA protein initiates chromosomal replication: evidnece from a mutant DnaA protein defective in regulatory ATP hydrolysis in vitro and in vivoQ38292172
Interaction of the initiator protein DnaA of Escherichia coli with its DNA targetQ38293364
Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins.Q38293922
Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication originQ38303508
Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK.Q38317649
ATP- and ADP-dnaA protein, a molecular switch in gene regulation.Q38318935
Protein-DNA interactions at a yeast replication originQ38328826
Site-directed mutational analysis for the membrane binding of DnaA protein. Identification of amino acids involved in the functional interaction between DnaA protein and acidic phospholipidsQ38332214
Requirements for and regulation of origin opening of plasmid P1.Q38333505
Site-directed mutational analysis for the ATP binding of DnaA protein. Functions of two conserved amino acids (Lys-178 and Asp-235) located in the ATP-binding domain of DnaA protein in vitro and in vivo.Q38334670
Autophosphorylation of archaeal Cdc6 homologues is regulated by DNA.Q39504873
The DnaC helicase loader is a dual ATP/ADP switch proteinQ39647456
Chaperone proteins abrogate inhibition of the human papillomavirus (HPV) E1 replicative helicase by the HPV E2 proteinQ39681443
DNA-binding domain of the RepE initiator protein of mini-F plasmid: involvement of the carboxyl-terminal regionQ39836320
Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motifQ40397137
Acidic phospholipids with unsaturated fatty acids inhibit the binding of origin recognition complex to origin DNA.Q40741051
The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time.Q41016426
Two steps to binding replication origins? DNA-protein interactions.Q41110842
Protein quality control: triage by chaperones and proteasesQ41433862
Archaea and the Origin(s) of DNA Replication ProteinsQ41524701
Origin DNA-binding proteinsQ41728296
Negative control of DNA replication by hydrolysis of ATP bound to DnaA protein, the initiator of chromosomal DNA replication in Escherichia coliQ42120466
Protein domains and conformational changes in the activation of RepA, a DNA replication initiatorQ42651088
Prediction of the structure of the replication initiator protein DnaA.Q42655710
Cdc18 transcription and proteolysis couple S phase to passage through mitosisQ42655828
Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2.Q42661197
Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA proteinQ42669406
Regulation of DNA replication by iterons: an interaction between the ori2 and incC regions mediated by RepE-bound iterons inhibits DNA replication of mini-F plasmid in Escherichia coliQ42677439
Molecular mechanism for functional interaction between DnaA protein and acidic phospholipids: identification of important amino acidsQ43511068
DNA replication-coupled inactivation of DnaA protein in vitro: a role for DnaA arginine-334 of the AAA+ Box VIII motif in ATP hydrolysisQ43579568
Mutational analysis of conserved sequence motifs in the budding yeast Cdc6 proteinQ43605563
Inhibitory module of Ets-1 allosterically regulates DNA binding through a dipole-facilitated phosphate contactQ43786814
The localized melting of mini-F origin by the combined action of the mini-F initiator protein (RepE) and HU and DnaA of Escherichia coliQ44029616
Human Hsp70 and Hsp40 chaperone proteins facilitate human papillomavirus-11 E1 protein binding to the origin and stimulate cell-free DNA replicationQ44770612
Activation of the herpes simplex virus type-1 origin-binding protein (UL9) by heat shock proteinsQ45734783
Allosteric effects of DNA on transcriptional regulatorsQ46483901
Nucleotide-dependent prereplicative complex assembly by Cdc6p, a homolog of eukaryotic and prokaryotic clamp-loadersQ47693928
Yeast origin recognition complex is involved in DNA replication and transcriptional silencingQ48093039
Linkage of replication to start by the Cdk inhibitor Sic1.Q51114804
Replication dynamics of the yeast genome.Q52053905
Nucleosomes positioned by ORC facilitate the initiation of DNA replication.Q52542122
The interaction domains of the DnaA and DnaB replication proteins of Escherichia coli.Q52969912
Analysis of the DNA-binding domain of Escherichia coli DnaA protein.Q52971588
Functional domains of DnaA proteins.Q52975761
Transcription of repA, the gene of the initiation protein of the Pseudomonas plasmid pPS10, is autoregulated by interactions of the RepA protein at a symmetrical operator.Q54012553
The DnaK chaperone system facilitates 30S ribosomal subunit assembly.Q54540763
Cooperative action of Escherichia coli ClpB protein and DnaK chaperone in the activation of a replication initiation protein.Q54549149
Conformational transition of DnaA protein by ATP: structural analysis of DnaA protein, the initiator of Escherichia coli chromosome replication.Q54569361
Ordered and sequential binding of DnaA protein to oriC, the chromosomal origin of Escherichia coli.Q54585074
Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae patovar savastanoi.Q54684492
Roles of Escherichia coli heat shock proteins DnaK, DnaJ and GrpE in mini-F plasmid replication.Q54719572
Reconciling the many faces of lateral gene transfer.Q55035590
Bacterial zipperQ59003148
AAA+ superfamily ATPases: common structure--diverse functionQ28208908
Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replicationQ28209282
The origin recognition complex: from simple origins to complex functionsQ28210087
Interactions between two catalytically distinct MCM subgroups are essential for coordinated ATP hydrolysis and DNA replicationQ28210357
Replication from oriP of Epstein-Barr virus requires human ORC and is inhibited by gemininQ28213116
ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complexQ28241786
Mechanistic aspects of DnaA-RepA interaction as revealed by yeast forward and reverse two-hybrid analysisQ28345862
Separate SCF(CDC4) recognition elements target Cdc6 for proteolysis in S phase and mitosis.Q28348429
Mutations in DnaA protein suppress the growth arrest of acidic phospholipid-deficient Escherichia coli cellsQ28354843
Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNAQ28360242
AAA proteins: in search of a common molecular basis. International Meeting on Cellular Functions of AAA ProteinsQ28364398
Coupling of local folding to site-specific binding of proteins to DNAQ29616464
Winged helix proteinsQ29617630
Whose end is destruction: cell division and the anaphase-promoting complexQ29618257
Two steps in the assembly of complexes at yeast replication origins in vivoQ29618323
Mcm2 is a target of regulation by Cdc7-Dbf4 during the initiation of DNA synthesisQ29976898
SV40 large T antigen hexamer structure: domain organization and DNA-induced conformational changesQ30309106
An overview of structural genomics.Q30327582
Proteomics: a technology-driven and technology-limited discovery scienceQ30668652
Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data?Q30690999
Clamp loaders and sliding clampsQ31048743
Genome trees and the tree of lifeQ31103613
Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteinsQ33694025
The nature of the last universal common ancestorQ33801540
Horizontal gene transfer and the origin of species: lessons from bacteria.Q33856631
Mechanistic studies of initiator-initiator interaction and replication initiationQ33889438
Control of plasmid DNA replication by iterons: no longer paradoxicalQ33912684
ATPase switches controlling DNA replication initiation.Q33912857
Ten commandments: lessons from the enzymology of DNA replicationQ33941332
In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication originQ33944339
Searching for the common ancestorQ33949864
The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 proteinQ33949872
Did evolution leap to create the protein universe?Q33960336
Plasmid rolling-circle replication: recent developmentsQ33994568
Phi29 family of phagesQ34010356
P433issue5
P921main subjectArchaeaQ10872
phylogeneticsQ171184
P304page(s)533-554
P577publication date2003-01-01
P1433published inFEMS Microbiology ReviewsQ15762226
P1476titleCommon domains in the initiators of DNA replication in Bacteria, Archaea and Eukarya: combined structural, functional and phylogenetic perspectives
P478volume26

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cites work (P2860)
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Q36852282Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP.

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