1qry - Revision history

OCA at 09:02, 22 May 2024

2024-05-22T09:02:22Z

←Older revision		Revision as of 09:02, 22 May 2024
Line 19:		Line 19:
	</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/main_output.php?pdb_ID=1qry ConSurf].		</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/main_output.php?pdb_ID=1qry ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The three-dimensional solution structure obtained by NMR of the A35T mutant vnd/NK-2 homeodomain bound to the vnd/NK-2 consensus 16 bp DNA sequence was determined. This mutation to threonine from alanine in position 35 in helix II of the vnd/NK-2 homeodomain is associated with early embryonic lethality in Drosophila melanogaster. Although the unbound mutant protein is not structured, in the DNA-bound state it adopts the three-helix fold characteristic of all known homeodomains, but with alterations relative to the structure of the wild-type analogue. These structural modifications occur, and are accompanied by a 50-fold reduction in the DNA binding affinity, even though most of the protein-DNA interactions originally seen for the wild-type homeodomain are found likewise in the threonine analogue. Alterations include torsional angle changes in the loop between helix I and helix II, and in the turn between helix II and helix III, as well as in a distortion of the usual antiparallel orientation of helix I with respect to helix II. The alteration of the position of leucine 40 in the A35T mutant is proposed to explain the observed 1.27 ppm upfield shift of the corresponding amide proton resonance relative to the value observed for the wild-type analogue. A detailed comparison of the structures of the mutant A35T and wild-type vnd/NK-2 homeodomains bound to the cognate DNA is presented. The consequences of the structural alteration of the DNA-bound A35T mutant vnd/NK-2 protein may constitute the basis of the observed early embryonic lethality.
		+
		+	Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.,Hwang KJ, Xiang B, Gruschus JM, Nam KY, No KT, Nirenberg M, Ferretti JA Biochemistry. 2003 Nov 4;42(43):12522-31. PMID:14580198<ref>PMID:14580198</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1qry" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:06, 17 April 2024

2024-04-17T06:06:49Z

←Older revision		Revision as of 06:06, 17 April 2024
Line 1:		Line 1:

	==Homeobox protein VND (ventral nervous system defective protein)==		==Homeobox protein VND (ventral nervous system defective protein)==
-	<StructureSection load='1qry' size='340' side='right'caption='[[1qry~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1qry' size='340' side='right'caption='[[1qry]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Drome Drome~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [https://pdbe.org/1qry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [https://www.ebi.ac.uk/pdbsum/1qry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qry ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [https://pdbe.org/1qry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [https://www.ebi.ac.uk/pdbsum/1qry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/VND_DROME VND_DROME]] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.	+	[https://www.uniprot.org/uniprot/VND_DROME VND_DROME] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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/main_output.php?pdb_ID=1qry ConSurf].		</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/main_output.php?pdb_ID=1qry ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The three-dimensional solution structure obtained by NMR of the A35T mutant vnd/NK-2 homeodomain bound to the vnd/NK-2 consensus 16 bp DNA sequence was determined. This mutation to threonine from alanine in position 35 in helix II of the vnd/NK-2 homeodomain is associated with early embryonic lethality in Drosophila melanogaster. Although the unbound mutant protein is not structured, in the DNA-bound state it adopts the three-helix fold characteristic of all known homeodomains, but with alterations relative to the structure of the wild-type analogue. These structural modifications occur, and are accompanied by a 50-fold reduction in the DNA binding affinity, even though most of the protein-DNA interactions originally seen for the wild-type homeodomain are found likewise in the threonine analogue. Alterations include torsional angle changes in the loop between helix I and helix II, and in the turn between helix II and helix III, as well as in a distortion of the usual antiparallel orientation of helix I with respect to helix II. The alteration of the position of leucine 40 in the A35T mutant is proposed to explain the observed 1.27 ppm upfield shift of the corresponding amide proton resonance relative to the value observed for the wild-type analogue. A detailed comparison of the structures of the mutant A35T and wild-type vnd/NK-2 homeodomains bound to the cognate DNA is presented. The consequences of the structural alteration of the DNA-bound A35T mutant vnd/NK-2 protein may constitute the basis of the observed early embryonic lethality.
-
-	Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.,Hwang KJ, Xiang B, Gruschus JM, Nam KY, No KT, Nirenberg M, Ferretti JA Biochemistry. 2003 Nov 4;42(43):12522-31. PMID:14580198<ref>PMID:14580198</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1qry" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Xiang, B]]	+	[[Category: Xiang B]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna-binding protein]]~~	+
-	~~[[Category: Helix-turn-helix~~]]	+

OCA at 10:02, 15 September 2021

2021-09-15T10:02:36Z

←Older revision		Revision as of 10:02, 15 September 2021
Line 3:		Line 3:
	<StructureSection load='1qry' size='340' side='right'caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1qry' size='340' side='right'caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1QRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [~~http~~://pdbe.org/1qry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1qry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1qry ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [https://pdbe.org/1qry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [https://www.ebi.ac.uk/pdbsum/1qry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/VND_DROME VND_DROME]] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.	+	[[https://www.uniprot.org/uniprot/VND_DROME VND_DROME]] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:08, 4 December 2019

2019-12-04T11:08:29Z

←Older revision		Revision as of 11:08, 4 December 2019
Line 1:		Line 1:

	==Homeobox protein VND (ventral nervous system defective protein)==		==Homeobox protein VND (ventral nervous system defective protein)==
-	<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1qry' size='340' side='right'caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Drome]]		[[Category: Drome]]
		+	[[Category: Large Structures]]
	[[Category: Xiang, B]]		[[Category: Xiang, B]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

OCA at 07:33, 28 February 2018

2018-02-28T07:33:28Z

←Older revision		Revision as of 07:33, 28 February 2018
Line 1:		Line 1:
		+
	==Homeobox protein VND (ventral nervous system defective protein)==		==Homeobox protein VND (ventral nervous system defective protein)==
	<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://pdbe.org/1qry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://pdbe.org/1qry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qry ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qr/1qry_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qr/1qry_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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].	+	</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/main_output.php?pdb_ID=1qry ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 32:		Line 33:
	[[Category: Drome]]		[[Category: Drome]]
	[[Category: Xiang, B]]		[[Category: Xiang, B]]
		+	[[Category: Dna binding protein]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

OCA at 21:32, 11 September 2015

2015-09-11T21:32:35Z

←Older revision		Revision as of 21:32, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Drosophila_melanogaster Drosophila melanogaster~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://pdbe.org/1qry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1qry" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drosophila melanogaster~~]]	+	[[Category: Drome]]
	[[Category: Xiang, B]]		[[Category: Xiang, B]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

OCA at 19:59, 25 December 2014

2014-12-25T19:59:10Z

←Older revision		Revision as of 19:59, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
-	</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=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VND_DROME VND_DROME]] Probable transcriptional regulator involved in the regulation of the proneural AS-C genes and the neurogenic genes of the enhancer of split complex. Could specifically activate proneural genes in the ventral-most neuroectoderm.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
-	[[Category: Xiang, B.]]	+	[[Category: Xiang, B]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

OCA at 14:52, 29 September 2014

2014-09-29T14:52:42Z

←Older revision		Revision as of 14:52, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1qry.~~png\|left~~\|200px]]	+	==Homeobox protein VND (ventral nervous system defective protein)==
		+	<StructureSection load='1qry' size='340' side='right' caption='[[1qry]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QRY FirstGlance]. <br>
		+	</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=1qry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qry RCSB], [http://www.ebi.ac.uk/pdbsum/1qry 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/qr/1qry_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 three-dimensional solution structure obtained by NMR of the A35T mutant vnd/NK-2 homeodomain bound to the vnd/NK-2 consensus 16 bp DNA sequence was determined. This mutation to threonine from alanine in position 35 in helix II of the vnd/NK-2 homeodomain is associated with early embryonic lethality in Drosophila melanogaster. Although the unbound mutant protein is not structured, in the DNA-bound state it adopts the three-helix fold characteristic of all known homeodomains, but with alterations relative to the structure of the wild-type analogue. These structural modifications occur, and are accompanied by a 50-fold reduction in the DNA binding affinity, even though most of the protein-DNA interactions originally seen for the wild-type homeodomain are found likewise in the threonine analogue. Alterations include torsional angle changes in the loop between helix I and helix II, and in the turn between helix II and helix III, as well as in a distortion of the usual antiparallel orientation of helix I with respect to helix II. The alteration of the position of leucine 40 in the A35T mutant is proposed to explain the observed 1.27 ppm upfield shift of the corresponding amide proton resonance relative to the value observed for the wild-type analogue. A detailed comparison of the structures of the mutant A35T and wild-type vnd/NK-2 homeodomains bound to the cognate DNA is presented. The consequences of the structural alteration of the DNA-bound A35T mutant vnd/NK-2 protein may constitute the basis of the observed early embryonic lethality.

-	~~{{STRUCTURE_1qry\| PDB=1qry \| SCENE= }}~~	+	Distortion of the three-dimensional structure of the vnd/NK-2 homeodomain bound to DNA induced by an embryonically lethal A35T point mutation.,Hwang KJ, Xiang B, Gruschus JM, Nam KY, No KT, Nirenberg M, Ferretti JA Biochemistry. 2003 Nov 4;42(43):12522-31. PMID:14580198<ref>PMID:14580198</ref>

-	~~===Homeobox protein VND (ventral nervous system defective protein)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14580198}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1qry]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Drosophila_melanogaster Drosophila melanogaster]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:014580198<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Xiang, B.]]		[[Category: Xiang, B.]]
	[[Category: Dna-binding protein]]		[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]

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

2013-01-02T09:44:48Z

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

←Older revision

Revision as of 09:44, 2 January 2013

OCA at 09:44, 2 January 2013

2013-01-02T09:44:42Z

←Older revision		Revision as of 09:44, 2 January 2013
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-	{{Seed}}
	[[Image:1qry.png\|left\|200px]]		[[Image:1qry.png\|left\|200px]]

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	{{STRUCTURE_1qry\| PDB=1qry \| SCENE= }}		{{STRUCTURE_1qry\| PDB=1qry \| SCENE= }}

	===Homeobox protein VND (ventral nervous system defective protein)===		===Homeobox protein VND (ventral nervous system defective protein)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14580198}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_14580198}}		{{ABSTRACT_PUBMED_14580198}}

	==About this Structure==		==About this Structure==
-	~~1QRY~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA].	+	[[1qry]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QRY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14580198~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014580198</ref><references group="xtra"/>
	[[Category: Drosophila melanogaster]]		[[Category: Drosophila melanogaster]]
	[[Category: Xiang, B.]]		[[Category: Xiang, B.]]
		+	[[Category: Dna-binding protein]]
	[[Category: Helix-turn-helix]]		[[Category: Helix-turn-helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:27:15 2009''