User:Wayne Decatur/kink-turn motif: Difference between revisions
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SEE PUBLIC DRAFT ==> [[Kink-turn_motif|HERE!!!]]<br> | |||
WHEN MADE INTO AN OFFICIAL PAGE:<br> | WHEN MADE INTO AN OFFICIAL PAGE:<br> | ||
* LINK FROM RNA motifs PAGE!!!! | * LINK FROM RNA motifs PAGE!!!! | ||
* Fix links from and to large ribosomal subunit (AND RIBOSOME?) page | |||
* Fix link from topic pages and from table of contents | * Fix link from topic pages and from table of contents | ||
* add Redirect from K-turn motif | * add Redirect from K-turn motif | ||
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==Introduction== | ==Introduction== | ||
<table width= | <table width=280' align='right' cellpadding='0'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><applet load='Image:Kt7.pdb.gz' size='280' frame='true' align='right' scene='User:Wayne_Decatur/kink-turn_motif/Ktcylinders/5' pspeed = '8'/></td></tr><tr><td bgcolor='#eeeeee'><center> | ||
{{Button Toggle NucleicDrumsColorScheme}} {{ColorKey Bases RNA}} | {{Button Toggle NucleicDrumsColorScheme}} {{ColorKey Bases RNA}} | ||
</center></td></tr></table> | </center></td></tr></table> | ||
Originally identified in the course of analyzing the [[Large Ribosomal Subunit of Haloarcula|large ribosomal subunit]]<ref name="kleinref">PMID: 11483524</ref>, this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif <ref>PMID: 11497434</ref> | [[kink-turn motif|The kink-turn motif]] is a common RNA structural motif that consists of helix–internal loop–helix motif that introduces a very tight kink into the helical axis, as illustrated in the figure below and 3D structure window on the right. Originally identified in the course of analyzing the [[Large Ribosomal Subunit of Haloarcula|large ribosomal subunit]]<ref name="kleinref">PMID: 11483524</ref>, this RNA structural motif was also identified in other RNAs. Particular instances have been called the GA motif <ref>PMID: 11497434</ref>. | ||
[[Image:Kink-turn.png|center|419px]]<br> | |||
The kink-turn motif includes the [[A-minor motif]]. | The kink-turn motif includes the [[A-minor motif]]. | ||
Many kink-turns bind proteins; however, that trait is not universal. They can mediate RNA tertiary structure interactions as well. | Many kink-turns bind proteins; however, that trait is not universal. They can mediate RNA tertiary structure interactions as well. | ||
An excellent introduction can be found [http://www.dundee.ac.uk/biocentre/nasg/kturn/index.php here as part of a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase">PMID: 20562215</ref>. | An excellent introduction can be found [http://www.dundee.ac.uk/biocentre/nasg/kturn/index.php here as part of a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase">PMID: 20562215</ref>. | ||
Kink-turns fall into two conformational classes, called N3 and N1. The classes differ in the pattern of hydrogen bonding in the core, and that pattern is determined by the basepair adjacent to the G•A pairs<ref name="classdeterm">PMID: 27016741</ref>. | |||
==Structures Containing the Motif== | ==Structures Containing the Motif== | ||
{{Kinkturnapplet}} | {{Kinkturnapplet}} | ||
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] contains 9 identified kink-turns<ref name="kleinref" /><ref name="lilleydatabase" />: <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7withproteins/9'>Kt-7</scene> and Kt-7 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7withproteins/10'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt15/2'>Kt-15</scene> and Kt-15 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt15/3'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt38/2'>Kt-38</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt42/5'>Kt-42</scene> and Kt-42 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt42/6'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt46/2'>Kt-46</scene> and Kt-46 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt46/3'>with bound proteins</scene>); <scene name='User:Wayne_Decatur/kink-turn_motif/Kt58/3'>Kt-58</scene> and Kt-58 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt58/4'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt4slash5/2'>Kt-4/5</scene> and Kt-4/5 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt4slash5/5'>with bound protein</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt94slash99/2'>Kt-94/99</scene> and Kt-94/99 with <scene name='User:Wayne_Decatur/kink-turn_motif/Kt94slash99/3'>bound protein</scene> of [[3cc2]]; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt78/2'>Kt-78</scene> as observed in [[ | * [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]]: | ||
:* <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/7'>The location of the eight kink-turns</scene> observed in the solved structure of [[Large Ribosomal Subunit of Haloarcula|the Haloarcula large ribosomal subunit]] shows they are on the surface of the subunit: <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt7/1'>Kt-7</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt15/1'>Kt-15</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt42/1'>Kt-42</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt46/1'>Kt-46</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt58/1'>Kt-58</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns4slash5/1'>Kt-4/5</scene>, | :* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] contains 9 identified kink-turns<ref name="kleinref" /><ref name="lilleydatabase" />: <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7withproteins/9'>Kt-7</scene> and Kt-7 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt7withproteins/10'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt15/2'>Kt-15</scene> and Kt-15 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt15/3'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt38/2'>Kt-38</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt42/5'>Kt-42</scene> and Kt-42 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt42/6'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt46/2'>Kt-46</scene> and Kt-46 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt46/3'>with bound proteins</scene>); <scene name='User:Wayne_Decatur/kink-turn_motif/Kt58/3'>Kt-58</scene> and Kt-58 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt58/4'>with bound proteins</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt4slash5/2'>Kt-4/5</scene> and Kt-4/5 <scene name='User:Wayne_Decatur/kink-turn_motif/Kt4slash5/5'>with bound protein</scene>; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt94slash99/2'>Kt-94/99</scene> and Kt-94/99 with <scene name='User:Wayne_Decatur/kink-turn_motif/Kt94slash99/3'>bound protein</scene> of [[3cc2]]; <scene name='User:Wayne_Decatur/kink-turn_motif/Kt78/2'>Kt-78</scene> as observed in [[4v5e]] (While present based on sequence comparison, Kt-78 is in a portion of the large subunit not visible in the crystal structure of [[3cc2]].) | ||
:* <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/7'>The location of the eight kink-turns</scene> observed in the solved structure of [[Large Ribosomal Subunit of Haloarcula|the Haloarcula large ribosomal subunit]] shows they are on the surface of the subunit: <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt7/1'>Kt-7</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt15/1'>Kt-15</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/8'>Kt-38</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt42/1'>Kt-42</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt46/1'>Kt-46</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturnskt58/1'>Kt-58</scene>, <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns4slash5/1'>Kt-4/5</scene>, and <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns94slash99/2'>Kt-94/99</scene>. (A ninth kink-turn, Kt-78, though present in ''Haloarcula marismortui'' rRNA is in a portion not resolved in the actual ''Haloarcula marismortui'' structure, yet is also on the surface.) | |||
:* See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on [http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_known.php this page at a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase" />. | :* See all of the 23S rRNA kink-turns and others on this page in greater detail following the appropriate links on [http://www.dundee.ac.uk/biocentre/nasg/kturn/kturns_known.php this page at a structural database for k-turn motifs in RNA by the Lilley group]<ref name="lilleydatabase" />. | ||
* The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment ([[1e7k]])<ref name="u4xstal">PMID: 11163207</ref>. The fact both the box C/D small nucleolar RNAs and the spliceosomal U4 RNA share this motif, and in fact bind the same protein, was observed<ref>PMID: 11081632</ref><ref name="u4xstal" /> even before the kink-turn was shown to be a widespread motif. | * The human spliceosomal and small nucleolar RNA-binding 15.5kD protein bound to the kink-turn of a U4 spliceosomal RNA fragment ([[1e7k]])<ref name="u4xstal">PMID: 11163207</ref>. The fact both the box C/D small nucleolar RNAs and the spliceosomal U4 RNA share this motif, and in fact bind the same protein, was observed<ref>PMID: 11081632</ref><ref name="u4xstal" /> even before the kink-turn was shown to be a widespread [[RNA motifs|RNA motif]]. | ||
* The <scene name=' | * The <scene name='User:Wayne_Decatur/kink-turn_motif/Proteincolored/1'>box C/D RNP</scene> from ''Sulfolobus solfataricus'' has two kink-turns that are bound by L7Ae ([[3pla]])<ref>PMID: 21270896</ref>. {{Link Toggle FancyCartoonHighQualityView}}. | ||
* ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae ([[1rlg]])<ref>PMID: 15130473</ref> | * ''A. fulgidus'' small ribonucleoprotein particle box C/D RNA has a kink-turn that is bound by L7Ae ([[1rlg]])<ref>PMID: 15130473</ref>. | ||
* ''Pyrococcus furiosus'' small ribonucleoprotein particle box H/ACA RNA ([[2hvy]]<ref>PMID: 16943774</ref>,[[3hax]],[[3hay]]<ref>PMID: 19481523</ref>) has a kink turn that is bound directly by L7ae in a complex of several proteins. | * ''Pyrococcus furiosus'' small ribonucleoprotein particle box H/ACA RNA ([[2hvy]]<ref>PMID: 16943774</ref>,[[3hax]],[[3hay]]<ref>PMID: 19481523</ref>) has a kink turn that is bound directly by L7ae in a complex of several proteins. | ||
* | * In the ''Pyrococcus furiosus'' small ribonucleoprotein particle structure a box C/D RNA has two kink-turns bound by L7Ae ([[3nvm]], [[3nvk]], [[3nvi]], and [[3nmu]])<ref>PMID: 20864039</ref>. | ||
* ''S. | * L7Ae protein as a subunit of archaeal RNase P binds to two kink-turns in the ''Pyrococcus furiosus'' RNase P RNA<ref>PMID: 25361963</ref>, <ref>PMID: 20675586</ref> | ||
* [[Azoarcus group I intron]]: | |||
:*The ''Azoarcus'' group I intron ([[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], and [[3iin]])<ref>PMID: 15175762</ref><ref>PMID: 16141079</ref><ref> PMID:18408159</ref><ref>PMID:20145044</ref> has a 'reverse' kink-turn. Overlay of the ''Azoarcus'' group I intron reverse kink-turn with a typical one (Kt-7) clearly illustrates the difference. '''PUT A SCENE HERE OF ALIGNMENT OF THIS WITH KT-7 with each Kt colored differently''' | |||
:* <scene name='User:Wayne_Decatur/kink-turn_motif/3cc2withkiturns/7'>The location of the single kink-turn</scene> highlighted within the solved structure of the''Azoarcus'' group I intron. | |||
* ''S. cerevisiae'' L30e bound to its pre-mRNA ([[1t0k]])<ref>PMID: 15242593</ref> has a kink-turn with a protein bound. | |||
* S-adenosylmethionine [[riboswitch]] regulatory mRNA element from ''Thermoanaerobacter tengcongensis'' ([[2gis]])<ref>PMID: 16810258</ref> has a kink-turn. | * S-adenosylmethionine [[riboswitch]] regulatory mRNA element from ''Thermoanaerobacter tengcongensis'' ([[2gis]])<ref>PMID: 16810258</ref> has a kink-turn. | ||
* The lysine [[riboswitch]] regulatory mRNA element from '' Thermotoga maritima'' ([[3dox]]) has a kink-turn | * The lysine [[riboswitch]] regulatory mRNA element from '' Thermotoga maritima'' ([[3dox]]) has a kink-turn | ||
* [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''<ref> PMID:11733066</ref> | * [[1nkw]] – The Large Ribosomal Subunit From ''Deinococcus radiodurans''<ref> PMID:11733066</ref> | ||
* The small ribosomal subunit ([[ | * The small ribosomal subunit ([[4v5e]]) has two kink-turns. | ||
==See Also== | ==See Also== | ||
* [[RNA motifs]] | * [[RNA motifs]] | ||
* [[Ribosome]] | * [[Ribosome]] | ||
* [[Large Ribosomal Subunit of Haloarcula|The Large Ribosomal Subunit]] | |||
* [[Ribozyme]] | |||
* [[Group I intron]] | |||
* [[Azoarcus group I intron]] | |||
* [[1go1]], [[1go0]], [[1w3e]] and [[1h7m]] – the ''Thermococcus celer'' ribosomal protein L30<ref>PMID: 12627951</ref><ref>PMID: 12824494</ref> | * [[1go1]], [[1go0]], [[1w3e]] and [[1h7m]] – the ''Thermococcus celer'' ribosomal protein L30<ref>PMID: 12627951</ref><ref>PMID: 12824494</ref> | ||
* A-minor motif | * A-minor motif | ||
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[[Category: tunnel]] | [[Category: tunnel]] | ||
[[Category: ribozyme]] | [[Category: ribozyme]] | ||
[[Category: ribosome]] | |||
[[Category: Rna-rna]] | [[Category: Rna-rna]] | ||
[[Category: 50S]] | [[Category: 50S]] | ||
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[[Category: Rrna-binding]] | [[Category: Rrna-binding]] | ||
[[Category: riboswitch]] | [[Category: riboswitch]] | ||
