1w29 - Revision history

OCA at 09:09, 9 May 2024

2024-05-09T09:09:35Z

←Older revision		Revision as of 09:09, 9 May 2024
Line 3:		Line 3:
	<StructureSection load='1w29' size='340' side='right'caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1w29' size='340' side='right'caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w19\|1w19]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [https://pdbe.org/1w29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [https://www.ebi.ac.uk/pdbsum/1w29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w29 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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [https://pdbe.org/1w29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [https://www.ebi.ac.uk/pdbsum/1w29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w29 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>	+	[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Riboflavin synthase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Bacher, A]]	+	[[Category: Bacher A]]
-	[[Category: Cushman, M]]	+	[[Category: Cushman M]]
-	[[Category: Fischer, M]]	+	[[Category: Fischer M]]
-	[[Category: Haase, I]]	+	[[Category: Haase I]]
-	[[Category: Illarionov, B]]	+	[[Category: Illarionov B]]
-	[[Category: Ladenstein, R]]	+	[[Category: Ladenstein R]]
-	[[Category: Meining, W]]	+	[[Category: Meining W]]
-	[[Category: Morgunova, E]]	+	[[Category: Morgunova E]]
-	~~[[Category: Inhibitor binding]]~~	+
-	~~[[Category: Lumazine synthase]]~~	+
-	~~[[Category: Riboflavin biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:06, 28 April 2021

2021-04-28T06:06:13Z

←Older revision		Revision as of 06:06, 28 April 2021
Line 3:		Line 3:
	<StructureSection load='1w29' size='340' side='right'caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1w29' size='340' side='right'caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1W29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1w19\|1w19]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [~~http~~://pdbe.org/1w29 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1w29 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1w29 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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [https://pdbe.org/1w29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [https://www.ebi.ac.uk/pdbsum/1w29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w29 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>	+	[[https://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:33, 10 April 2019

2019-04-10T07:33:40Z

←Older revision		Revision as of 07:33, 10 April 2019
Line 1:		Line 1:

	==Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate==		==Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate==
-	<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1w29' size='340' side='right'caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
Line 34:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]

OCA at 07:52, 4 April 2018

2018-04-04T07:52:56Z

←Older revision		Revision as of 07:52, 4 April 2018
Line 1:		Line 1:
-	==~~LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO~~ 3-(1,3,7-~~TRIHYDRO~~-9-D-~~RIBITYL~~-2,6,8-~~PURINETRIONE~~-7-YL) ~~BUTANE~~ 1-~~PHOSPHATE~~==	+
		+	==Lumazine Synthase from Mycobacterium tuberculosis bound to 3-(1,3,7- trihydro-9-D-ribityl-2,6,8-purinetrione-7-yl)butane 1-phosphate==
	<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://pdbe.org/1w29 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://pdbe.org/1w29 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w29 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/w2/1w29_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w2/1w29_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=1w29 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:41, 11 September 2015

2015-09-11T15:41:20Z

←Older revision		Revision as of 15:41, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://pdbe.org/1w29 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 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 1w29" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]

OCA at 18:32, 25 December 2014

2014-12-25T18:32:02Z

←Older revision		Revision as of 18:32, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
-	[[Category: Bacher, A.]]	+	[[Category: Bacher, A]]
-	[[Category: Cushman, M.]]	+	[[Category: Cushman, M]]
-	[[Category: Fischer, M.]]	+	[[Category: Fischer, M]]
-	[[Category: Haase, I.]]	+	[[Category: Haase, I]]
-	[[Category: Illarionov, B.]]	+	[[Category: Illarionov, B]]
-	[[Category: Ladenstein, R.]]	+	[[Category: Ladenstein, R]]
-	[[Category: Meining, W.]]	+	[[Category: Meining, W]]
-	[[Category: Morgunova, E.]]	+	[[Category: Morgunova, E]]
	[[Category: Inhibitor binding]]		[[Category: Inhibitor binding]]
	[[Category: Lumazine synthase]]		[[Category: Lumazine synthase]]
	[[Category: Riboflavin biosynthesis]]		[[Category: Riboflavin biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 11:27, 3 October 2014

2014-10-03T11:27:31Z

←Older revision		Revision as of 11:27, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1w29\| PDB=1w29 \| SCENE= }}~~	+	==LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) BUTANE 1-PHOSPHATE==
-	===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) BUTANE 1-PHOSPHATE===	+	<StructureSection load='1w29' size='340' side='right' caption='[[1w29]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	{{~~ABSTRACT_PUBMED_15723519}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W29 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=TS0:4-{2,6,8-TRIOXO-9-[(2S,3R,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS0</scene>, <scene name='pdbligand=TS1:4-{2,6,8-TRIOXO-9-[(2R,3S,4R)-2,3,4,5-TETRAHYDROXYPENTYL]-1,2,3,6,8,9-HEXAHYDRO-7H-PURIN-7-YL}BUTYL+DIHYDROGEN+PHOSPHATE'>TS1</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w19\|1w19]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] </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=1w29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w29 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1w29 RCSB], [http://www.ebi.ac.uk/pdbsum/1w29 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/w2/1w29_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 enzymes involved in the biosynthesis of riboflavin represent attractive targets for the development of drugs against bacterial pathogens, because the inhibitors of these enzymes are not likely to interfere with enzymes of the mammalian metabolism. Lumazine synthase catalyzes the penultimate step in the riboflavin biosynthesis pathway. A number of substituted purinetrione compounds represent a new class of highly specific inhibitors of lumazine synthase from Mycobacterium tuberculosis. To develop potent antibiotics for the treatment of tuberculosis, we have determined the structure of lumazine synthase from M. tuberculosis in complex with two purinetrione inhibitors and have studied binding via isothermal titration calorimetry. The structures were determined by molecular replacement using lumazine synthase from Saccharomyces cerevisiae as a search model and refined at 2 and 2.3 A resolution. The R-factors were 14.7 and 17.4%, respectively, and the R(free) values were 19.3 and 26.3%, respectively. The enzyme was found to be a pentamer consisting of five subunits related by 5-fold local symmetry. The comparison of the active site architecture with the active site of previously determined lumazine synthase structures reveals a largely conserved topology with the exception of residues Gln141 and Glu136, which participate in different charge-charge interactions in the core space of the active site. The impact of structural changes in the active site on the altered binding and catalytic properties of the enzyme is discussed. Isothermal titration calorimetry measurements indicate highly specific binding of the purinetrione inhibitors to the M. tuberculosis enzyme with dissociation constants in micromolar range.

-	~~==Function==~~	+	Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors.,Morgunova E, Meining W, Illarionov B, Haase I, Jin G, Bacher A, Cushman M, Fischer M, Ladenstein R Biochemistry. 2005 Mar 1;44(8):2746-58. PMID:15723519<ref>PMID:15723519</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-~~8~~-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino~~)~~uracil with 3,4-dihydroxy-2-butanone 4~~-~~phosphate. This is the penultimate step in the biosynthesis of riboflavin~~.<ref>PMID:15723519</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1w29]] is~~ a ~~5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:015723519</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]

OCA at 08:52, 23 April 2014

2014-04-23T08:52:09Z

←Older revision		Revision as of 08:52, 23 April 2014
Line 1:		Line 1:
-	[[Image:1w29.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1w29", 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_1w29\| PDB=1w29 \| SCENE= }}		{{STRUCTURE_1w29\| PDB=1w29 \| SCENE= }}
-
	===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) BUTANE 1-PHOSPHATE===		===LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL) BUTANE 1-PHOSPHATE===
		+	{{ABSTRACT_PUBMED_15723519}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/RISB_MYCTU RISB_MYCTU]] Catalyzes the formation of 6,7-dimethyl-8-ribityllumazine by condensation of 5-amino-6-(D-ribitylamino)uracil with 3,4-dihydroxy-2-butanone 4-phosphate. This is the penultimate step in the biosynthesis of riboflavin.<ref>PMID:15723519</ref>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_15723519}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~), ~~where 15723519~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_15723519}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:015723519</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015723519</ref><references group="xtra"/><references/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]

OCA: Protected "1w29" [edit=sysop:move=sysop]

2011-08-24T06:51:20Z

Protected "1w29" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:51, 24 August 2011

OCA at 06:51, 24 August 2011

2011-08-24T06:51:17Z

←Older revision		Revision as of 06:51, 24 August 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1w29.png\|left\|200px]]		[[Image:1w29.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1W29~~ is a 5 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA].	+	[[1w29]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W29 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15723519~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015723519</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Riboflavin synthase]]		[[Category: Riboflavin synthase]]
Line 34:		Line 33:
	[[Category: Meining, W.]]		[[Category: Meining, W.]]
	[[Category: Morgunova, E.]]		[[Category: Morgunova, E.]]
-	[[Category: ~~Crystal structure,mycobacterium tuberculosis,inhibitor~~ binding~~,x-ray diffraction~~]]	+	[[Category: Inhibitor binding]]
-	[[Category: ~~Transferase,riboflavin biosynthesis,lumazine~~ synthase]]	+	[[Category: Lumazine synthase]]
-		+	[[Category: Riboflavin biosynthesis]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Wed Feb 18 02~~:~~34:15 2009''~~	+	[[Category: Transferase]]