Image Pseudoknot.svg thumb 300px This example of a naturally occurring pseudoknot is found in the RNA component of human telomerase . Sequence from. ref name Chen Chen JL, Greider CW. 2005 . Functional analysis of the pseudoknot structure in human telomerase RNA . Proc Natl Acad Sci USA 102 23 8080 5. ref Image Pseudoknot 1YMO.png thumb 300px Threedimensional structure of a pseudoknot from a human telomerase RNA. A sticks B backbone. The pdb file is based on PDB 1YMO . NOTOC A pseudoknot is a nucleic acid secondary structure containing at least two stem loop structures in which half of one stem is intercalated between the two halves of another stem. The pseudoknot was first recognized in the turnip yellow mosaic virus in 1982. ref name Staple cite journal author Staple DW, Butcher SE title Pseudoknots RNA structures with diverse functions journal PLoS Biol. volume 3 issue 6 pages e213 year 2005 month June pmid 15941360 pmc 1149493 doi 10.1371 journal.pbio.0030213 url http dx.plos.org 10.1371 journal.pbio.0030213 accessdate 2010 07 15 ref Pseudoknots fold into knot shaped three dimensional conformations but are not true knot mathematics topological knots . Prediction and identification The structural configuration of pseudoknots does not lend itself well to bio computational detection ... compbio rnafold Pfold will not predict pseudoknot structures present in a query sequence they will only identify the more stable of the two pseudoknot stems. It is possible to identify a limited class ... complete . ref name Lyngso Lyngs RB, Pedersen CN. 2000 . RNA pseudoknot prediction in energy ... of pseudoknot prediction in simple models. Paper presented at the ICALP. ref Biological significance ... RNA component contains a pseudoknot that is critical for activity. ref name Chen Several viruses use a pseudoknot structure to form a tRNA like motif to infiltrate the host cell. ref name ... doi 10.1093 nar 13.5.1717 pmc 341107 ref The pseudoknot region of RNase P is one of the most conserved ... more details
Infobox rfam Name ALIL pseudoknot image ALIL pk.png width caption Secondary structure of ALIL without the pseudoknot Symbol ALIL AltSymbols Rfam RF01497 RNA type Cis reg Tax domain Bacteria ALIL pseudoknot is an RNA element that induces frameshift ing in bacteria. The expression of a minority of gene s requires frameshifting to occur where the frequency of frameshifting is increased by a RNA secondary structure located on the 3 side of the shift site. This structure can be either a pseudoknot or a stem loop and acts as a physical barrier to mRNA Chromosomal translocation translocation so therefore causes ribosome pausing. ref name pmid12762025 Cite pmid 12762025 ref ALIL pseudoknot was identified though comparative analysis of the a class of transposable elements belonging to the insertion sequence 3 IS3 family and is shown to be conservation genetics conserved across a number of bacteria species. ref name pmid8029330 Cite pmid 8029330 ref This pseudoknot stimulates programmed 1 ribosomal frameshifting PRF 1 which in turn stimulates the express of transposase , an enzyme required for transposition. Mutagenesis and RNA structure probing chemical probing were used to determine the secondary structure of this pseudoknot and it has been proposed that this pseudoknot is formed by interactions between an apical loop and internal loop. ref name pmid18474594 Cite pmid 18474594 ref References reflist External links Rfam id RF01497 name ALIL pseudoknot Category RNA Category Bacteria ... more details
Infobox rfam Name Prion pseudoknot image RF00523.jpg width caption Predicted secondary structure and sequence conservation of Prion pknot Symbol Prion pknot AltSymbols Rfam RF00523 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Eukaryota GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The prion pseudoknot is predicted cis regulatory element RNA pseudoknot structure found in prion protein mRNA . ref cite journal last Wills first PR title Potential pseudoknots in the PrP encoding mRNA. journal Journal of Theoretical Biology date 1992 Dec 21 volume 159 issue 4 pages 523 7 pmid 1296103 doi 10.1016 S0022 5193 05 80696 4 ref It has been suggested that this element has a possible effect in prion protein translation . ref name Bar01 cite journal last Barrette first I coauthors Poisson G, Gendron P, Major F year 2001 title Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching journal Nucleic Acids Res volume 29 pages 753&ndash 758 pmid 11160898 doi 10.1093 nar 29.3.753 issue 3 pmc 30388 ref The human prion protein contains 5 copies of a 24 nucleotide repeat that contains this structure. ref name Bar01 References reflist 1 External links Rfam id RF00523 name Prion pseudoknot Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name Coronavirus 3 UTR pseudoknot image RF00165.jpg width caption Predicted secondary structure and sequence conservation of Corona pk3 Symbol Corona pk3 AltSymbols Rfam RF00165 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000205 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Coronavirus 3 UTR pseudoknot is an RNA structure found in the coronavirus genome. Coronaviruses contain 30 kb single stranded positive sense RNA genome s. The three prime untranslated region 3 UTR region of these coronavirus genomes contains a conserved 55 nucleotide pseudoknot structure which is necessary for viral genome replication. ref cite journal last Williams first GD coauthors Chang RY, Brian DA year 1999 title A phylogenetically conserved hairpin type 3 untranslated region pseudoknot functions in coronavirus RNA replication journal J Virol volume 73 pages 8349&ndash 8355 pmid 10482585 issue 10 pmc 112852 ref The mechanism of cis regulatory cis regulation is unclear, but this element is postulated to function in the plus strand. Other RNA families identified in the coronavirus include the coronavirus SL III cis acting replication element CRE , the coronavirus frameshifting stimulation element , the coronavirus 3 stem loop II like motif s2m and the coronavirus packaging signal . References reflist 1 External links Rfam id RF00165 name Coronavirus 3 UTR pseudoknot Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name Influenza Pseudoknot image PK.png width 226px caption The consensus secondary structure of the Influenza Pseudoknot family of RNA motifs Symbol PK IAV AltSymbols Rfam RF01099 RNA type Cis reg Tax domain Orthomyxoviridae CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Influenza virus pseudoknot is an RNA pseudoknot secondary structure structure formed in one of the non structural coding region coding segments NS of influenza virus genome . ref name R10 cite journal author Gultyaev AP, Olsthoorn RC title A family of non classical pseudoknots in influenza A and B viruses journal RNA Biol volume 7 issue 2 pages 125 9 year 2010 month March pmid 20200490 doi url http www.landesbioscience.com journals rna abstract.php?id 11287 accessdate 2010 07 13 ref Pseudoknots are commonly found in viral genome genomes , especially RNA virus RNA viruses , where they can have a wide range of functions. ref name nature cite journal author Brierley I, Pennell S, Gilbert RJ title Viral RNA pseudoknots versatile motifs in gene expression and replication journal Nat. Rev. Microbiol. volume 5 issue 8 pages 598 610 year 2007 month August pmid 17632571 doi 10.1038 nrmicro1704 url accessdate 2010 07 13 ref The orientation of the coaxially stacked stems in the influenza pseudoknot, however, differs from the most common topology in classical RNA pseudoknots. ref cite journal author Pleij CW title Pseudoknots a new motif in the RNA game journal Trends Biochem. Sci. volume 15 issue 4 pages 143 7 year 1990 month April pmid 1692647 doi url accessdate 2010 07 13 ref ref cite doi 10.1016 S0959 440X 94 90101 5 ref The pseudoknot structure is very similar in influenzavirus A and influenzavirus B . A unique point mutation occurring in the strains of influenza A virus subtype H5N1 after 2001 has been suggested to result in RNA conformational shift, ref ... an alternative stem loop hairpin structure instead of the pseudoknot. ref name R10 See Also Non ... more details
Infobox rfam Name Long range pseudoknot image RF01086.png width 200 caption Secondary structure of the long range pseudoknot Symbol AltSymbols Rfam RF01086 miRBase miRBase family RNA type Cis reg Tax domain Eukaryote Prokaryote CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData A long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control. A long range pseudoknot is thought to negatively regulate the translation of the IF3 L35 L20 operon in E. coli . This operon encodes the translation factor 3 IF3 and ribosomal proteins L35 and L20. In this example, the RNA RNA interaction occurs between nucleotides separated by a 300 nucleotide loop region. ref cite journal title A long range RNA RNA interaction forms a pseudoknot required for translational control of the IF3 L35 L20 ribosomal protein operon in Escherichia coli journal EMBO J year 1996 first C last Chiaruttini coauthors M Milet, M Springer volume 15 16 issue 16 pages 4402 13 pmid 8861967 pmc 452164 ref A long range pseudoknot is also believed to be required for the activity of the Neurospora VS ribozyme . ref cite journal title A long range pseudoknot is required for activity of the Neurospora VS ribozyme journal EMBO J year 1996 first T last Rastogi coauthors T L Beattie, J E Olive, and R A Collins volume 15 11 issue 11 pages 2820 25 pmid 8654379 pmc 450219 ref References Reflist External links http rfam.sanger.ac.uk family RF01086 Rfam entry for Long range pseudoknots Category Non coding RNA ... more details
Infobox rfam Name Pseudoknot of the regulatory region of the repBA gene image RF01089.png width 200 caption Secondary structure of the pseudoknot of the regulatory region of the repBA gene Symbol AltSymbols Rfam RF01089 miRBase miRBase family RNA type Cis reg Tax domain Eukaryotes Prokaryotes CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData In plasmids , the regulatory region of repBA gene forms a pseudoknot . The repA gene , which encodes a protein likely to function as an initiator for DNA replication replication , and the repB gene are Translation biology translationally coupled. The Leader sequence mRNA leader sequence of the repA mRNA contains two complementary sequences of 8 bases. Base pair Base pairing between these two sequences forms a pseudoknot which is essential for translation. The first of these complementary sequences is found within a stem loop , which forms a target for RNAI . Binding of RNAI to this stem loop inhibits pseudoknot formation and translation of RepA. ref name pmid7543895 cite journal author Athanasopoulos V, Praszkier J, Pittard AJ title The replication of an IncL M plasmid is subject to antisense control journal J. Bacteriol. volume 177 issue 16 pages 4730 41 year 1995 month August pmid 7543895 pmc 177239 doi url ref ref name pmid10074073 cite journal author Athanasopoulos V, Praszkier J, Pittard AJ title Analysis of elements involved in pseudoknot dependent expression and regulation of the repA gene of an IncL M plasmid journal J. Bacteriol. volume 181 issue 6 pages 1811 9 year 1999 month March pmid 10074073 pmc 93579 doi url ref References Reflist External links http rfam.sanger.ac.uk family RF01089 Rfam entry for Regulatory region of repBA gene Category Non coding RNA ... more details
Infobox rfam Name Alpha operon ribosome binding site image RF00140.jpg width caption Predicted secondary structure and sequence conservation of Alpha RBS Symbol Alpha RBS AltSymbols Rfam RF00140 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The alpha operon ribosome binding site in bacteria is surrounded by this complex pseudoknot ted RNA structure. Translation of the mRNA produces 4 ribosomal protein products, one of which S4 acts as a translational repressor by binding to the nested pseudoknot region. The mechanism of repression is thought to involve a conformational switch in the pseudoknot region and ribosome entrapment. ref cite journal last Schlax first PJ coauthors Xavier KA, Gluick TC, Draper DE year 2001 title Translational repression of the Escherichia coli alpha operon mRNA importance of an mRNA conformational switch and a ternary entrapment complex journal J Biol Chem volume 276 pages 38494&ndash 38501 pmid 11504736 doi 10.1074 jbc.M106934200 issue 42 ref References reflist 1 External links Rfam id RF00140 name Alpha operon ribosome binding site Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name Interferon gamma 5 UTR regulatory element image RF00259.jpg width caption Predicted secondary structure and sequence conservation of IFN gamma Symbol IFN gamma AltSymbols Rfam RF00259 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Eukaryota GO SO SO 0000204 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Interferon gamma 5 UTR regulatory elements are a family of regulatory RNA s. This family represents a pseudoknot containing stem loop structure found in the 5 UTR of interferon gamma mRNA. This structure is thought to be involved in translational regulation and the pseudoknot has been found to activate protein kinase R PKR which is known to be a translational inhibitor. Mutations in the pseudoknot structure have been found to reduce PKR activation and increase the translation of interferon gamma. ref cite journal last Ben Asouli first Y coauthors Banai Y, Pel Or Y, Shir A, Kaempfer R year 2002 title Human interferon gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon inducible protein kinase PKR journal Cell volume 108 pages 221&ndash 232 pmid 11832212 doi 10.1016 S0092 8674 02 00616 5 issue 2 ref References reflist 1 External links Rfam id RF00259 name Interferon gamma 5 UTR regulatory element Category Cis regulatory RNA elements molecular cell biology stub ... more details
Orphan date October 2010 Infobox rfam Name Regulatory region of repZ gene image RF01087.png width 200 caption Secondary structure of the regulatory region of repZ gene Symbol repZ AltSymbols Rfam RF01087 miRBase miRBase family RNA type Cis reg Tax domain Proteobacteria CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The regulatory region of the repZ gene , which encodes the replication initiator of plasmid ColIb P9, contains a pseudoknot . This acts as a molecular switch controlling translation of repZ and repY. ref cite journal title An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIalpha plasmid ColIb P9. journal J Biol Chem year 2003 first k last Asano K coauthors K Mizobuchi volume 273 pages 11815 25 pmid 9565606 issue 19 doi 10.1074 jbc.273.19.11815 ref References Reflist External links http rfam.sanger.ac.uk family RF01087 Rfam entry for Regulatory region of repZ gene Category Non coding RNA ... more details
2006 Each of the viral RNA molecules contains four hair pin structures and a pseudoknot in the 3 UTR . The pseudoknot is unusual in that it contains a small stem loop structure inside loop L1. ref ... pseudoknot in SPCSV http rfam.sanger.ac.uk family RF01095 Rfam entry for 3 terminal pseudoknot of CuYV BPYV http rfam.sanger.ac.uk family RF01078 Rfam entry for 3 terminal pseudoknot in PYVV Navbox ... list1 Gallery lines 4 Image RF01091.png 3 terminal pseudoknot in SPCSV Predicted secondary structure ... RF01091 . Image RF01078.png 3 terminal pseudoknot in PYVV Predicted secondary structure taken ... . Image RF01095.png 3 terminal pseudoknot of CuYV BPYV Predicted secondary structure taken from the http ... more details
Infobox rfam Name Coronavirus frameshifting stimulation element image RF00507.jpg width caption Predicted secondary structure and sequence conservation of Corona FSE Symbol Corona FSE AltSymbols Rfam RF00507 miRBase miRBase family RNA type Cis regulatory element Cis reg Translational frameshift frameshift element Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData In molecular biology , the coronavirus Translational frameshift frameshifting stimulation element is a sequence alignment conserved stem loop of RNA found in coronavirus es that can promote ribosome ribosomal Translational frameshift frameshifting . Such RNA molecules interact with a downstream region to form a pseudoknot structure the region varies according to the virus but pseudoknot formation is known to stimulate Translational frameshift frameshifting . In the classical situation, a sequence 32 nucleotide s downstream of the stem is complementary to part of the loop. In other coronaviruses, however, another stem loop structure around 150 nucleotides downstream can interact with members of this family to form kissing stem loop s and stimulate frameshifting. ref cite journal last Baranov first PV coauthors Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT year 2005 title Programmed ribosomal frameshifting in decoding the SARS CoV genome journal Virology volume 332 pages 498&ndash 510 pmid 15680415 doi 10.1016 j.virol.2004.11.038 issue 2 ref Other RNA families identified in the coronavirus include the Coronavirus SL III cis acting replication element CRE SL III cis acting replication element CRE , the coronavirus 3 stem loop II like motif s2m , the coronavirus packaging signal and the coronavirus 3 UTR pseudoknot . References reflist 1 External links Rfam id RF00507 name Coronavirus frameshifting stimulation element Category Cis regulatory RNA elements molecular cell biology stub ... more details
Orphan date April 2012 Gag pol translational readthrough site or Retroviral readthrough element is a cis regulatory element found in retroviruses. ref name pmid8076609 cite journal author Wills NM, Gesteland RF, Atkins JF title Pseudoknot dependent read through of retroviral gag termination codons importance of sequences in the spacer and loop 2 journal EMBO J. volume 13 issue 17 pages 4137 44 year 1994 month September pmid 8076609 pmc 395336 doi url ref The readthrough site facilitates the mechanism of translation genetics translation readthrough of the stop codon at the gag pol junction producing the gag and pol fusion protein in certain retrovirus es. Retroviruses whose gag and pol genes are in the same reading frame often depend upon approximately 5 read through of the gag UAG termination codon to form the gag pol polyprotein. This readthrough is usually dependent on a pseudoknot located eight nucleotides downstream of the stop codon UAG . Sequence conservation is found in the second pseudoknot loop. Navbox name hide the gallery title Gallery of secondary structure images titlestyle background e7dcc3 state autocollapse list1 Gallery lines 6 Image GP knot1 secondary structure.jpg GP knot1 Secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01073 RF01073 . Derived from Pseudobase http www.ekevanbatenburg.nl PKBASE PKB00047.HTML PKB00047 http www.ekevanbatenburg.nl PKBASE PKB00078.HTML PKB00078 http www.ekevanbatenburg.nl PKBASE PKB00079.HTML PKB00079 http www.ekevanbatenburg.nl PKBASE PKB00088.HTML PKB00088 http www.ekevanbatenburg.nl PKBASE PKB00098.HTML PKB00098 http www.ekevanbatenburg.nl PKBASE PKB00099.HTML PKB00099 Image GP knot2 secondary structure.jpg GP knot2 Secondary structure taken from the http rfam.sanger.ac.uk Rfam database. Family http rfam.sanger.ac.uk family RF01092 RF01092 . Derived from Pseudobase http www.ekevanbatenburg.nl PKBASE PKB00048.HTML PKB00048 References reflist External lin ... more details
Infobox rfam Name Ribosomal S15 leader image RF00114.jpg width caption Predicted secondary structure and sequence conservation of S15 Symbol S15 AltSymbols Rfam RF00114 miRBase miRBase family RNA type Cis regulatory element Cis reg leader Tax domain Bacteria GO SO SO 0005836 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The E. coli ribosomal S15 leader is an cis regulatory element RNA element that can form two alternative structures found in the ribosomal S15 protein. One of the two alternate structures is a series of three stem loop hairpins , the other includes a pseudoknot . ref cite journal last Benard first L coauthors Philippe C, Ehresmann B, Ehresmann C, Portier C year 1996 title Pseudoknot and translational control in the expression of the S15 ribosomal protein journal Biochimie volume 78 pages 568&ndash 576 pmid 8955900 doi 10.1016 S0300 9084 96 80003 4 issue 7 ref This structure causes translational regulation of the S15 protein . Only the final two hairpins are conserved in other species. See also Ribosomal protein L20 leader References reflist 1 External links Rfam id RF00114 name Ribosomal S15 leader Category ribosomal protein leader molecular cell biology stub ... more details
The Varkud satellite VS ribozyme is an RNA enzyme that carries out the cleavage of a phosphodiester bond. ref cite journal author Saville BJ, Collins RA title A site specific self cleavage reaction performed by a novel RNA in Neurospora ribozymes journal Cell volume 61 issue 4 pages 685 696 year 1990 doi 10.1016 0092 8674 90 90480 3 pmid 2160856 ref ref name pmid14730013 cite journal author Lilley DM title The Varkud satellite ribozyme journal RNA volume 10 issue 2 pages 151 8 year 2004 month February pmid 14730013 pmc 1370526 doi 10.1261 rna.5217104 url ref Structure The VS ribozyme is composed of 5 helices that form an H shape helices II to VI . The first helix I contains the substrate cleavage site in the stem loop . The activity of the VS ribozyme is thought to require a long range pseudoknots long range pseudoknot structure. ref cite journal title A long range pseudoknot is required for activity of the Neurospora VS ribozyme. journal EMBO J year 1996 first T last Rastogi coauthors T L Beattie, J E Olive, and R A Collins volume 15 11 issue 11 pages 2820 25 pmid 8654379 pmc 450219 ref Species distribution The VS ribozyme has only been found in mitochondrial DNA of Neurospora . References references molecular cell biology stub Category Ribozymes Category Non coding RNA Category RNA splicing ... more details
Infobox rfam Name Antizyme RNA frameshifting stimulation element image RF00381.jpg width caption Predicted secondary structure and sequence conservation of Antizyme FSE Symbol Antizyme FSE AltSymbols Rfam RF00381 miRBase miRBase family RNA type Cis regulatory element Cis reg Translational frameshift frameshift element Tax domain Eukaryota GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Antizyme RNA frameshifting stimulation element is a Cis regulatory element structural element which is found in Ornithine decarboxylase antizyme antizyme mRNA and is known to promote Translational frameshift frameshifting . Antizyme genes have two partially overlapping open reading frame s, the second, which encodes the functional protein requires 1 translational frameshifting. This frameshift is stimulated by a pseudoknot present 3 of the frameshift site in the antizyme mRNA. The frameshifting efficiency is dependent on the level of polyamine s in the cell, when the polyamine concentration is high frameshifting is more likely to occur which leads to an increase in the quantity of functional antizyme produced. The functional antizyme acts to reduce ornithine decarboxylase ODC activity which leads to a drop in polyamines present in the cell. Therefore, this family can be thought of as a biosensor for intracellular free polyamines ref cite journal author Ivanov IP, Anderson CB, Gesteland RF, Atkins JF title Identification of a new antizyme mRNA 1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species. journal J Mol Biol volume 339 issue 3 pages 495 504 year 2004 pmid 15147837 doi 10.1016 j.jmb.2004.03.082 ref . References reflist 1 External links Rfam id RF00381 name Antizyme RNA frameshifting stimulation element DEFAULTSORT Antizyme Rna Frameshifting Stimulation Element Category Cis regulatory RNA elements molecular cell biology stub ... more details
Taxobox virus group iv familia Closteroviridae genus Crinivirus species Potato yellow vein virus The Potato yellow vein virus PYVV is a plant pathogen of the Closteroviridae family. It is a whitefly transmitted closterovirus vectored by Trialeurodes vaporariorum , which is known to cause a yellowing disease in potato crops in South America ref name pmid15218192 Cite journal author Livieratos IC, Eliasco E, M ller G, et al. title Analysis of the RNA of Potato yellow vein virus evidence for a tripartite genome and conserved 3 terminal structures among members of the genus Crinivirus journal J. Gen. Virol. volume 85 issue Pt 7 pages 2065 75 year 2004 month July pmid 15218192 doi 10.1099 vir.0.79910 0 url ref . PYVV RNA have a conserved 3 terminal secondary structure, which includes a pseudoknot ref name pmid15218192 . References Reflist 1 Category Viruses Category Viral plant pathogens and diseases virus stub fr Virus des nervures jaunes de la pomme de terre ... more details
Infobox rfam Name UPSK RNA image RF00390.jpg width caption Predicted secondary structure and sequence conservation of UPSK Symbol UPSK AltSymbols Rfam RF00390 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Upstream pseudoknot UPSK domain is an cis regulatory element RNA element found in the turnip yellow mosaic virus , beet virus Q ref name pmid9714254 cite journal author Koenig R, Pleij CW, Beier C, Commandeur U title Genome properties of beet virus Q, a new furo like virus from sugarbeet, determined from unpurified virus journal J. Gen. Virol. volume 79 issue 8 pages 2027 36 year 1998 month August pmid 9714254 doi url http vir.sgmjournals.org cgi pmidlookup?view long&pmid 9714254 ref , barley stripe mosaic virus ref name pmid8623558 cite journal author Solovyev AG, Savenkov EI, Agranovsky AA, Morozov SY title Comparisons of the genomic cis elements and coding regions in RNA beta components of the hordeiviruses barley stripe mosaic virus, lychnis ringspot virus, and poa semilatent virus journal Virology volume 219 issue 1 pages 9 18 year 1996 month May pmid 8623558 doi 10.1006 viro.1996.0217 url ref and tobacco mosaic virus ref name pmid8608444 cite journal author Felden B, Florentz C, Gieg R, Westhof E title A central pseudoknotted three way junction imposes tRNA like mimicry and the orientation of three 5 upstream pseudoknots in the 3 terminus of tobacco mosaic virus RNA journal RNA volume 2 issue 3 pages 201 12 year 1996 month March pmid 8608444 pmc 1369363 doi url http www.rnajournal.org cgi pmidlookup?view long&pmid 8608444 ref , which is thought to be needed for efficient Transcription genetics transcription . Disruption of the pseudoknot structure gives rise to a 50 drop in transcription efficiency. ref cite journal last Deiman first BA coauthors Kortlever RM, Pleij CW year 1997 title The role of the pseudoknot at ... more details
are a pseudoknot ted structure. Most of these riboswitches conserve a kink turn structural motif that permits a bend in the relevant stem, presumably facilitating the pseudoknot. Several nucleotide positions are highly conserved, with many around the terminal loops involved in the pseudoknot ... more details
stacked helices arranged side by side. These stacks are held together by a pseudoknot formed between the loop on the end of stem P2 and the J3 4 joining region. The formation of the pseudoknot ... aptamer is determined by the formation of a K turn dependant pseudoknot journal Biochemistry ... and the pseudoknot are critical to the establishment of the global fold and productive binding. The binding ... downstream of the P1 stem and interacts, by a second pseudoknot, with P3, while the kink turn is absent ... loop in SAM I riboswitches forms a kink turn motif that allows the RNA to form a pseudoknot. The variant ... the SAM I like pseudoknot. See also SAM II riboswitch SMK box riboswitch SAM III riboswitch ... more details
Infobox rfam Name Pseudoknot of the domain G G12 of 23S ribosomal RNA image PK G12rRNA secondary structure.jpg width caption Predicted secondary structure and sequence conservation of PK G12rRNA Symbol PK G12rRNA AltSymbols Rfam RF01118 miRBase miRBase family RNA type Gene Ribosomal RNA rRNA Tax domain Bacteria GO SO SO 0001263 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Image PDB 1c2w EBI.png thumb 200px left A 3D representation of the ribosome. This is a view of the 3D arrangement of the 23S and 5S rRNA in the Escherichia coli 50S ribosomal subunit based on a Transmission electron microscopy cryo electron microscopic reconstruction . ref name pmid10756104 cite journal author Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, W hnert J, G rlach M, van Heel M, Brimacombe R title The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo electron microscopic reconstruction at 7.5 A resolution. journal J Mol Biol volume 298 issue 1 pages 35 59 year 2000 pmid 10756104 doi 10.1006 jmbi.2000.3635 ref Image PDB 2j28 EBI.jpg thumb 200px left A 3D representation of the ribosome. ref name pmid17086193 cite journal author Halic M, Blau M, Becker T, Mielke T, Pool MR, Wild K, Sinning I, Beckmann R title Following the signal sequence from ribosomal tunnel exit to signal recognition particle. journal Nature volume 444 issue 7118 pages 507 11 year 2006 pmid 17086193 doi 10.1038 nature05326 ref The 23S rRNA is a 2904 Nucleotide nt long in Escherichia coli E. coli component of the large prokaryotic subunit 50S The ribosomal peptidyl transferase activity resides in this rRNA. This is achieved by a base A2486 which the nitrogen at position 3 acts as a base and accepts the H from the amino group of the aa tRNA in the A site, the aa tRNA with its free electron nucleophile Nucleophilic acyl substitution ... ribosomal RNA http www.ekevanbatenburg.nl PKBASE PKB00148.HTML Pseudobase entry for pseudoknot of the 23S ... more details
be further classified, for example, tetraloop s, pseudoknot s, and stem loop s. Double helix Main Nucleic ... see also the List of RNA structure prediction software . Pseudoknots Main Pseudoknot Image Pseudoknot.svg thumb 499px This example of a naturally occurring pseudoknot is found in the RNA component of human ... JL, Greider CW. year 2005 title Functional analysis of the pseudoknot structure in human telomerase RNA url journal Proc Natl Acad Sci USA volume 102 issue 23 pages 8080 5 ref A pseudoknot is an RNA ... a pseudoknot that is critical for activity. ref name Chen Though DNA can also form pseudoknots ... detect pseudoknot s or other cases in which base pairs are not fully nested. More general methods ... more details
Infobox rfam Name Coronavirus SL III cis acting replication element CRE image RF00496.jpg width caption Predicted secondary structure and sequence conservation of Corona SL III Symbol Corona SL III AltSymbols Rfam RF00496 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000233 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The coronavirus SL III cis acting replication element CRE is an cis regulatory element RNA element that regulates defective interfering DI RNA replication . ref cite journal last Raman first S coauthors Bouma P, Williams GD, Brian DA year 2003 title Stem loop III in the 5 untranslated region is a cis acting element in bovine coronavirus defective interfering RNA replication journal J Virol volume 77 pages 6720&ndash 6730 pmid 12767992 doi 10.1128 JVI.77.12.6720 6730.2003 issue 12 pmc 156170 ref Other RNA families identified in the coronavirus include the coronavirus 3 stem loop II like motif s2m , the coronavirus frameshifting stimulation element , the coronavirus packaging signal and the coronavirus 3 UTR pseudoknot . See also Cardiovirus cis acting replication element CRE Citrus tristeza virus replication signal References reflist 1 External links Rfam id RF00496 name Coronavirus SL III cis acting replication element CRE Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name Enteroviral 3 UTR element image RF00041.jpg width caption Predicted secondary structure and sequence conservation of Entero OriR Symbol Entero OriR AltSymbols Rfam RF00041 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Virus es GO SO SO 0000205 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData In molecular biology , the enteroviral 3 UTR element is an RNA structure found in the Three prime untranslated region 3 UTR of various enterovirus es. The overall structure forms the origin of replication OriR for the initiation of strand RNA synthesis . ref name wang 1999 cite journal last Wang first J coauthors Bakkers JM, Galama JM, Bruins Slot HJ, Pilipenko EV, Agol VI, Melchers WJ year 1999 title Structural requirements of the higher order RNA kissing element in the enteroviral 3 UTR journal Nucleic Acids Res volume 27 pages 485&ndash 490 pmid 9862969 doi 10.1093 nar 27.2.485 issue 2 pmc 148204 ref Pseudoknot s have also been predicted in this structure. ref name wang 1999 See also Enterovirus 5 cloverleaf cis acting replication element Enterovirus cis acting replication element References reflist 1 External links Rfam id RF00041 name Enteroviral 3 UTR element Category Cis regulatory RNA elements molecular cell biology stub ... more details
Encyclopedia
top
