1utf - Revision history

OCA: Redirecting to 4v4f

2014-12-10T15:00:09Z

Redirecting to 4v4f

← Older revision		Revision as of 15:00, 10 December 2014
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	~~==THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)==~~		#REDIRECT [[4v4f]] This PDB entry is obsolete and replaced by 4v4f
	~~<StructureSection load='1utf' size='340' side='right' caption='[[1utf]], [[Resolution\|resolution]] 1.90Å' scene=''>~~
	~~== Structural highlights ==~~
	<table><tr><td colspan='2'>[[1utf]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UTF FirstGlance]. <br>
	~~</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene><br>~~
	~~<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1utv\|1utv]], [[1c9s\|1c9s]], [[1gtf\|1gtf]], [[1gtn\|1gtn]], [[1qaw\|1qaw]], [[1utd\|1utd]]</td></tr>~~
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1utf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1utf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1utf RCSB], [http://www.ebi.ac.uk/pdbsum/1utf PDBsum]</span></td></tr>
	~~<table>~~
	~~== Evolutionary Conservation ==~~
	~~[[Image:Consurf_key_small.gif\|200px\|right]]~~
	~~Check<jmol>~~
	~~<jmolCheckbox>~~
	~~<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ut/1utf_consurf.spt"</scriptWhenChecked>~~
	~~<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>~~
	~~<text>to colour the structure by Evolutionary Conservation</text>~~
	~~</jmolCheckbox>~~
	~~</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the~~ [[~~Conservation%2C_Evolutionary\|explanation~~]] ~~of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].~~
	~~<div style="clear:both"></div>~~
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in several Bacilli by binding to the leader region of the nascent trp mRNA, inhibiting continued transcription. The 11 subunit TRAP molecule is active in complex with tryptophan, and binds consequently an RNA target segment consisting of 11 (G/U)AG triplets, each separated by two or three non-conserved "spacer" nucleotides. Here, we report the first crystal structures of TRAP in a complex with RNA containing UAG triplets separated by two nucleotides and in a complex with RNA containing GAG triplets separated by three nucleotides. Comparison with known structures of TRAP-RNA complexes shows that both substitution of G-1 with U-1 in the triplet and addition of an extra spacer nucleotide lead to a more flexible complex. This ~~suggests an explanation why, in the trp leader RNA, all three-nucleotide spacer regions are followed by a G-1 nucleotide. Taken together, the structures demonstrate that RNA binding to TRAP~~ is ~~mediated by specific interactions involving the A-2~~ and ~~G-3 nucleotides of the triplet. This is accompanied~~ by ~~the disruption of stacking interactions between the bases of the other nucleotides, contributing to the increase in entropy that drives binding.~~

	The interaction of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides.,Hopcroft NH, Manfredo A, Wendt AL, Brzozowski AM, Gollnick P, Antson AA J Mol Biol. 2004 Apr 16;338(1):43-53. PMID:15050822<ref>PMID:15050822</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~

	~~==See Also==~~
	*[[Tryptophan RNA-binding attenuation protein\|Tryptophan RNA-binding attenuation protein]]
	~~== References ==~~
	~~<references/>~~
	~~__TOC__~~
	~~</StructureSection>~~
	~~[[Category: Geobacillus stearothermophilus]]~~
	~~[[Category: Antson, A A.]]~~
	~~[[Category: Brzozowski, A M.]]~~
	~~[[Category: Gollnick, P.]]~~
	~~[[Category: Hopcroft, N H.]]~~
	~~[[Category: Manfredo, A.]]~~
	~~[[Category: Wendt, A L.]]~~
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Rna-binding protein]]~~
	~~[[Category: Transcription attenuation]]~~
	~~[[Category: Trp rna]]~~

OCA at 08:20, 3 October 2014

2014-10-03T08:20:04Z

@@ Line 1: / Line 1: @@
-{{STRUCTURE_1utf|  PDB=1utf  |  SCENE=  }}
+==THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)==
-===THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)===
+<StructureSection load='1utf' size='340' side='right' caption='[[1utf]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
-{{ABSTRACT_PUBMED_15050822}}
+== Structural highlights ==
-==About this Structure==
+The interaction of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides.,Hopcroft NH, Manfredo A, Wendt AL, Brzozowski AM, Gollnick P, Antson AA J Mol Biol. 2004 Apr 16;338(1):43-53. PMID:15050822<ref>PMID:15050822</ref>
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<ref group="xtra">PMID:015050822</ref><references group="xtra"/><references/>
+</div>
 [[Category: Geobacillus stearothermophilus]]
 [[Category: Antson, A A.]]

OCA at 08:15, 23 April 2014

2014-04-23T08:15:45Z

← Older revision		Revision as of 08:15, 23 April 2014
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	~~[[Image:1utf.png\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1utf", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_1utf\| PDB=1utf \| SCENE= }}		{{STRUCTURE_1utf\| PDB=1utf \| SCENE= }}

	===THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)===		===THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_15050822}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 15050822 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_15050822}}		{{ABSTRACT_PUBMED_15050822}}

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	==Reference==		==Reference==
	<ref group="xtra">PMID:015050822</ref><~~ref group="xtra">PMID:011914485</ref><ref~~ group="xtra"~~>PMID:010499579<~~/~~ref~~><references ~~group="xtra"~~/>		<ref group="xtra">PMID:015050822</ref><references group="xtra"/><references/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Antson, A A.]]		[[Category: Antson, A A.]]

OCA at 04:56, 24 August 2011

2011-08-24T04:56:27Z

← Older revision		Revision as of 04:56, 24 August 2011
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	==Reference==		==Reference==
	<ref group="xtra">PMID:~~15050822~~</ref><ref group="xtra">PMID:~~11914485~~</ref><ref group="xtra">PMID:~~10499579~~</ref><references group="xtra"/>		<ref group="xtra">PMID:015050822</ref><ref group="xtra">PMID:011914485</ref><ref group="xtra">PMID:010499579</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Antson, A A.]]		[[Category: Antson, A A.]]

OCA: Protected "1utf" [edit=sysop:move=sysop]

2011-03-14T12:38:07Z

Protected "1utf" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:38, 14 March 2011
(No difference)

OCA at 12:38, 14 March 2011

2011-03-14T12:38:05Z

← Older revision		Revision as of 12:38, 14 March 2011
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	~~{{Seed}}~~
	[[Image:1utf.png\|left\|200px]]		[[Image:1utf.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
	~~1UTF~~ is a 33 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTF OCA].		[[1utf]] is a 33 chain structure with sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTF OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:15050822</ref><references group="xtra"/>		<ref group="xtra">PMID:15050822</ref><ref group="xtra">PMID:11914485</ref><ref group="xtra">PMID:10499579</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	[[Category: Antson, A A.]]		[[Category: Antson, A A.]]
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	[[Category: Manfredo, A.]]		[[Category: Manfredo, A.]]
	[[Category: Wendt, A L.]]		[[Category: Wendt, A L.]]
			[[Category: Rna binding protein]]
	[[Category: Rna-binding protein]]		[[Category: Rna-binding protein]]
	[[Category: Transcription attenuation]]		[[Category: Transcription attenuation]]
	[[Category: Trp rna]]		[[Category: Trp rna]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:34:46 2009''~~

OCA at 13:34, 16 February 2009

2009-02-16T13:34:47Z

← Older revision		Revision as of 13:34, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	1UTF is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTF OCA].		1UTF is a 33 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UTF OCA].

	==Reference==		==Reference==
	The interaction of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides., Hopcroft NH, Manfredo A, Wendt AL, Brzozowski AM, Gollnick P, Antson AA, J Mol Biol. 2004 Apr 16;338(1):43-53. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~15050822 15050822]~~		<ref group="xtra">PMID:15050822</ref><references group="xtra"/>
	[[Category: Geobacillus stearothermophilus]]		[[Category: Geobacillus stearothermophilus]]
	~~[[Category: Protein complex]]~~
	[[Category: Antson, A A.]]		[[Category: Antson, A A.]]
	[[Category: Brzozowski, A M.]]		[[Category: Brzozowski, A M.]]
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	[[Category: Trp rna]]		[[Category: Trp rna]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 18~~:30:~~59 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 15:34:46 2009''

OCA at 15:31, 27 July 2008

2008-07-27T15:31:04Z

← Older revision		Revision as of 15:31, 27 July 2008
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	[[Image:1utf.~~gif~~\|left\|200px]]		{{Seed}}
			[[Image:1utf.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1utf\| PDB=1utf \| SCENE= }}		{{STRUCTURE_1utf\| PDB=1utf \| SCENE= }}

	~~'''~~THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)~~'''~~		===THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)===


	~~==Overview==~~		<!--
	The ~~trp RNA-binding attenuation protein (TRAP) regulates expression of~~ the ~~tryptophan biosynthetic genes in several Bacilli by binding~~ to the leader region of the nascent trp mRNA, inhibiting continued transcription. The 11 subunit TRAP molecule is active in complex with tryptophan, and binds consequently an RNA target segment consisting of 11 (G/~~U)AG triplets, each separated by two or three non-conserved "spacer" nucleotides~~. Here, we report the first crystal structures of TRAP in a complex with RNA containing UAG triplets separated by two nucleotides and in a complex with RNA containing GAG triplets separated by three nucleotides. Comparison with known structures of TRAP-RNA complexes shows that both substitution of G-1 with U-1 in the triplet and addition of an extra spacer nucleotide lead to a more flexible complex. This suggests an explanation why, in the ~~trp leader RNA, all three-nucleotide spacer regions are followed by a G-1 nucleotide~~. ~~Taken together, the structures demonstrate that RNA binding to TRAP is mediated by specific interactions involving the A~~-~~2 and G~~-~~3 nucleotides of the triplet. This is accompanied by the disruption of stacking interactions between the bases of the other nucleotides, contributing to the increase in entropy that drives binding.~~		The line below this paragraph, {{ABSTRACT_PUBMED_15050822}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 15050822 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_15050822}}

	==About this Structure==		==About this Structure==
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	[[Category: Transcription attenuation]]		[[Category: Transcription attenuation]]
	[[Category: Trp rna]]		[[Category: Trp rna]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 11~~:39:52 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:30:59 2008''

OCA at 08:39, 3 May 2008

2008-05-03T08:39:55Z

← Older revision		Revision as of 08:39, 3 May 2008
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	[[Image:1utf.gif\|left\|200px]]		[[Image:1utf.gif\|left\|200px]]

	{{Structure		<!--
	\|PDB~~= 1utf \|SIZE=350\|CAPTION= <scene name='initialview01'>1utf</~~scene>, ~~resolution 1~~.~~90Å~~		The line below this paragraph, containing "STRUCTURE_1utf", creates the "Structure Box" on the page.
	~~\|SITE= <scene name='pdbsite=AC1:TRP+Binding+Site+For+Chain+V'>AC1</scene>~~		You may change the PDB parameter (which sets the PDB file loaded into the applet)
	~~\|LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=G:GUANOSINE~~-~~5'~~-~~MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene~~>		or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
	\|~~ACTIVITY~~=		or leave the SCENE parameter empty for the default display.
	\|~~GENE~~=		-->
	~~\|DOMAIN=~~		{{STRUCTURE_1utf\| PDB=1utf \| SCENE= }}
	~~\|RELATEDENTRY=~~
	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1utf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1utf OCA], [http://www.ebi.ac.uk/pdbsum/1utf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1utf RCSB]</span>
	}}

	'''THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)'''		'''THE STRUCTURE OF THE TRP RNA-BINDING ATTENUATION PROTEIN (TRAP) BOUND TO A RNA MOLECULE CONTAINING UAGAU REPEATS (PART I)'''
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	[[Category: Manfredo, A.]]		[[Category: Manfredo, A.]]
	[[Category: Wendt, A L.]]		[[Category: Wendt, A L.]]
	[[Category: ~~rna~~-binding protein]]		[[Category: Rna-binding protein]]
	[[Category: ~~transcription~~ attenuation]]		[[Category: Transcription attenuation]]
	[[Category: ~~trp~~ rna]]		[[Category: Trp rna]]
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 11:39:52 2008''
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 00~~:14:59 2008''

OCA at 21:14, 30 March 2008

2008-03-30T21:14:59Z

← Older revision		Revision as of 21:14, 30 March 2008
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	\|PDB= 1utf \|SIZE=350\|CAPTION= <scene name='initialview01'>1utf</scene>, resolution 1.90Å		\|PDB= 1utf \|SIZE=350\|CAPTION= <scene name='initialview01'>1utf</scene>, resolution 1.90Å
	\|SITE= <scene name='pdbsite=AC1:TRP+Binding+Site+For+Chain+V'>AC1</scene>		\|SITE= <scene name='pdbsite=AC1:TRP+Binding+Site+For+Chain+V'>AC1</scene>
	\|LIGAND= <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>		\|LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
			\|DOMAIN=
			\|RELATEDENTRY=
			\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1utf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1utf OCA], [http://www.ebi.ac.uk/pdbsum/1utf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1utf RCSB]</span>
	}}		}}

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	[[Category: Manfredo, A.]]		[[Category: Manfredo, A.]]
	[[Category: Wendt, A L.]]		[[Category: Wendt, A L.]]
	~~[[Category: TRP]]~~
	[[Category: rna-binding protein]]		[[Category: rna-binding protein]]
	[[Category: transcription attenuation]]		[[Category: transcription attenuation]]
	[[Category: trp rna]]		[[Category: trp rna]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar 20 14:~~36:30~~ 2008''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:14:59 2008''