1xz8 - Revision history

OCA at 06:51, 23 August 2023

OCA — Wed, 23 Aug 2023 06:51:07 GMT

←Older revision		Revision as of 06:51, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1xz8' size='340' side='right'caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xz8' size='340' side='right'caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus~~ caldolyticus~~" heinen and heinen 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.8Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [https://pdbe.org/1xz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [https://www.ebi.ac.uk/pdbsum/1xz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xz8 ProSAT]</span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [https://pdbe.org/1xz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [https://www.ebi.ac.uk/pdbsum/1xz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PYRR_BACCL PYRR_BACCL]] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes (Probable). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.	+	[https://www.uniprot.org/uniprot/PYRR_BACCL PYRR_BACCL] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes (Probable). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus caldolyticus heinen and heinen 1972]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Uracil phosphoribosyltransferase]]~~	+	[[Category: Bonner HK]]
-	[[Category: Bonner~~, H K~~]]	+	[[Category: Chander P]]
-	[[Category: Chander, P]]	+	[[Category: Fields CJ]]
-	[[Category: Fields~~, C J~~]]	+	[[Category: Grabner GK]]
-	[[Category: Grabner~~, G K~~]]	+	[[Category: Halbig KM]]
-	[[Category: Halbig~~, K M~~]]	+	[[Category: Miller JK]]
-	[[Category: Miller~~, J K~~]]	+	[[Category: Smith JL]]
-	[[Category: Smith~~, J L~~]]	+	[[Category: Switzer RL]]
-	[[Category: Switzer~~, R L]]~~	+
-	~~[[Category: Attenuation protein]]~~	+
-	~~[[Category: Prtase]]~~	+
-	~~[[Category: Pyrimidine biosynthesis]]~~	+
-	~~[[Category: Rna-binding]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 16:21, 3 November 2021

OCA — Wed, 03 Nov 2021 16:21:48 GMT

←Older revision		Revision as of 16:21, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1xz8' size='340' side='right'caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xz8' size='340' side='right'caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus caldolyticus" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus caldolyticus" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [~~http~~://pdbe.org/1xz8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xz8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xz8 ProSAT]</span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [https://pdbe.org/1xz8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [https://www.ebi.ac.uk/pdbsum/1xz8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PYRR_BACCL PYRR_BACCL]] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes (Probable). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.	+	[[https://www.uniprot.org/uniprot/PYRR_BACCL PYRR_BACCL]] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes (Probable). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:52, 29 January 2020

OCA — Wed, 29 Jan 2020 16:52:19 GMT

←Older revision		Revision as of 16:52, 29 January 2020
Line 1:		Line 1:

	==Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form==		==Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form==
-	<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1xz8' size='340' side='right'caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus caldolyticus" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus caldolyticus" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus caldolyticus heinen and heinen 1972]]		[[Category: Bacillus caldolyticus heinen and heinen 1972]]
		+	[[Category: Large Structures]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
	[[Category: Bonner, H K]]		[[Category: Bonner, H K]]

OCA at 07:11, 18 April 2018

OCA — Wed, 18 Apr 2018 07:11:28 GMT

←Older revision		Revision as of 07:11, 18 April 2018
Line 1:		Line 1:
		+
	==Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form==		==Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form==
	<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'bacillus_caldolyticus~~' '~~bacillus caldolyticus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_caldolyticus"_heinen_and_heinen_1972 "bacillus caldolyticus" heinen and heinen 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://pdbe.org/1xz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum]</span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://pdbe.org/1xz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xz8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xz/1xz8_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xz/1xz8_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>
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus caldolyticus]]	+	[[Category: Bacillus caldolyticus heinen and heinen 1972]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
	[[Category: Bonner, H K]]		[[Category: Bonner, H K]]

OCA at 02:58, 10 February 2016

OCA — Wed, 10 Feb 2016 02:58:33 GMT

←Older revision		Revision as of 02:58, 10 February 2016
Line 18:		Line 18:
	<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=1xz8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:42, 11 September 2015

OCA — Fri, 11 Sep 2015 04:42:34 GMT

←Older revision		Revision as of 04:42, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_caldolyticus Bacillus~~ caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'bacillus_caldolyticus' 'bacillus caldolyticus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum]</span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://pdbe.org/1xz8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1xz8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:19, 25 December 2014

OCA — Thu, 25 Dec 2014 11:19:24 GMT

←Older revision		Revision as of 11:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum]</span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYRR_BACCL PYRR_BACCL]] Regulates transcriptional attenuation of the pyrimidine nucleotide (pyr) operon by binding in a uridine-dependent manner to specific sites on pyr mRNA. This disrupts an antiterminator hairpin in the RNA and favors formation of a downstream transcription terminator, leading to a reduced expression of downstream genes (Probable). Also displays a weak uracil phosphoribosyltransferase activity which is not physiologically significant.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Bacillus caldolyticus]]		[[Category: Bacillus caldolyticus]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
-	[[Category: Bonner, H K.]]	+	[[Category: Bonner, H K]]
-	[[Category: Chander, P.]]	+	[[Category: Chander, P]]
-	[[Category: Fields, C J.]]	+	[[Category: Fields, C J]]
-	[[Category: Grabner, G K.]]	+	[[Category: Grabner, G K]]
-	[[Category: Halbig, K M.]]	+	[[Category: Halbig, K M]]
-	[[Category: Miller, J K.]]	+	[[Category: Miller, J K]]
-	[[Category: Smith, J L.]]	+	[[Category: Smith, J L]]
-	[[Category: Switzer, R L.]]	+	[[Category: Switzer, R L]]
	[[Category: Attenuation protein]]		[[Category: Attenuation protein]]
	[[Category: Prtase]]		[[Category: Prtase]]
Line 47:		Line 49:
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Uracil phosphoribosyltransferase]]

OCA at 18:30, 29 September 2014

OCA — Mon, 29 Sep 2014 18:30:14 GMT

←Older revision		Revision as of 18:30, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xz8.~~png~~\|~~left~~\|200px]]	+	==Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form==
		+	<StructureSection load='1xz8' size='340' side='right' caption='[[1xz8]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XZ8 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3GP:GUANOSINE-3-MONOPHOSPHATE'>3GP</scene>, <scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a3c\|1a3c]], [[1non\|1non]], [[1xzn\|1xzn]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uracil_phosphoribosyltransferase Uracil phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.9 2.4.2.9] </span></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=1xz8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xz8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xz8 RCSB], [http://www.ebi.ac.uk/pdbsum/1xz8 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/xz/1xz8_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 ==
		+	PyrR is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. PyrR acts by binding to specific sequences on pyr mRNA and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. PyrR from Bacillus subtilis has been purified and extensively studied. In this work, we describe the purification to homogeneity and characterization of recombinant PyrR from the thermophile Bacillus caldolyticus and the crystal structures of unliganded PyrR and a PyrR-nucleotide complex. The B. caldolyticus pyrR gene was previously shown to restore normal regulation of the B. subtilis pyr operon in a pyrR deletion mutant. Like B. subtilis PyrR, B. caldolyticus PyrR catalyzes the uracil phosphoribosyltransferase reaction but with maximal activity at 60 degrees C. Crystal structures of B. caldolyticus PyrR reveal a dimer similar to the B. subtilis PyrR dimer and, for the first time, binding sites for nucleotides. UMP and GMP, accompanied by Mg2+, bind specifically to PyrR active sites. Nucleotide binding to PyrR is similar to other phosphoribosyltransferases, but Mg2+ binding differs. GMP binding was unexpected. The protein bound specific sequences of pyr RNA 100 to 1,000 times more tightly than B. subtilis PyrR, depending on the RNA tested and the assay method; uridine nucleotides enhanced RNA binding, but guanosine nucleotides antagonized it. The new findings of specific GMP binding and its antagonism of RNA binding suggest cross-regulation of the pyr operon by purines.

-	~~{{STRUCTURE_1xz8\| PDB=1xz8 \| SCENE= }}~~	+	Structure of the nucleotide complex of PyrR, the pyr attenuation protein from Bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides.,Chander P, Halbig KM, Miller JK, Fields CJ, Bonner HK, Grabner GK, Switzer RL, Smith JL J Bacteriol. 2005 Mar;187(5):1773-82. PMID:15716449<ref>PMID:15716449</ref>

-	~~===Pyrr~~, ~~The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15716449}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1xz8]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015716449<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus caldolyticus]]		[[Category: Bacillus caldolyticus]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]

OCA: Protected "1xz8" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:09:19 GMT

Protected "1xz8" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:09, 5 January 2013

OCA at 11:09, 5 January 2013

OCA — Sat, 05 Jan 2013 11:09:14 GMT

←Older revision		Revision as of 11:09, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xz8.png\|left\|200px]]		[[Image:1xz8.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xz8", 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_1xz8\| PDB=1xz8 \| SCENE= }}		{{STRUCTURE_1xz8\| PDB=1xz8 \| SCENE= }}

	===Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form===		===Pyrr, The Regulator Of The Pyrimidine Biosynthetic Operon In Bacillus caldolyticus, Nucleotide-bound form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15716449}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15716449 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15716449}}		{{ABSTRACT_PUBMED_15716449}}

	==About this Structure==		==About this Structure==
-	~~1XZ8~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA].	+	[[1xz8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_caldolyticus Bacillus caldolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XZ8 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15716449~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015716449</ref><references group="xtra"/>
	[[Category: Bacillus caldolyticus]]		[[Category: Bacillus caldolyticus]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
Line 38:		Line 26:
	[[Category: Pyrimidine biosynthesis]]		[[Category: Pyrimidine biosynthesis]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
		+	[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Uracil phosphoribosyltransferase]]		[[Category: Uracil phosphoribosyltransferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:52:27 2009''