1kz9 - Revision history

OCA at 18:13, 29 May 2024

OCA — Wed, 29 May 2024 18:13:25 GMT

←Older revision		Revision as of 18:13, 29 May 2024
Line 20:		Line 20:
	</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=1kz9 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=1kz9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.
		+
		+	The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.,Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M J Mol Biol. 2002 May 17;318(5):1317-29. PMID:12083520<ref>PMID:12083520</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1kz9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:05, 3 April 2024

OCA — Wed, 03 Apr 2024 08:05:08 GMT

←Older revision		Revision as of 08:05, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='1kz9' size='340' side='right'caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1kz9' size='340' side='right'caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 3.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>[https://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </~~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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [https://pdbe.org/1kz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz9 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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [https://pdbe.org/1kz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO]] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</ref>	+	[https://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1kz9 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=1kz9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.
-
-	The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.,Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M J Mol Biol. 2002 May 17;318(5):1317-29. PMID:12083520<ref>PMID:12083520</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kz9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
-	[[Category: Cbs 356]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bacher, A]]
-	[[Category: Cushman, M]]
-	[[Category: Fischer, M]]
-	[[Category: Gerhardt, S]]
-	[[Category: Haase, I]]
-	[[Category: Huber, R]]
-	[[Category: Kaiser, J T]]
-	[[Category: Steinbacher, S]]
-	[[Category: Ligand binding]]
-	[[Category: Lumazine synthase]]
-	[[Category: Riboflavin biosynthesis]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Bacher A]]
		+	[[Category: Cushman M]]
		+	[[Category: Fischer M]]
		+	[[Category: Gerhardt S]]
		+	[[Category: Haase I]]
		+	[[Category: Huber R]]
		+	[[Category: Kaiser JT]]
		+	[[Category: Steinbacher S]]

OCA at 06:37, 18 August 2021

OCA — Wed, 18 Aug 2021 06:37:25 GMT

←Older revision		Revision as of 06:37, 18 August 2021
Line 3:		Line 3:
	<StructureSection load='1kz9' size='340' side='right'caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1kz9' size='340' side='right'caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [~~http~~://pdbe.org/1kz9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kz9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz9 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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [https://pdbe.org/1kz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [https://www.ebi.ac.uk/pdbsum/1kz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO]] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</ref>	+	[[https://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO]] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:15, 13 November 2019

OCA — Wed, 13 Nov 2019 12:15:35 GMT

←Older revision		Revision as of 12:15, 13 November 2019
Line 1:		Line 1:

	==Mutant Enzyme L119F Lumazine Synthase from S.pombe==		==Mutant Enzyme L119F Lumazine Synthase from S.pombe==
-	<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='1kz9' size='340' side='right'caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
Line 36:		Line 36:
	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]		[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
	[[Category: Cbs 356]]		[[Category: Cbs 356]]
		+	[[Category: Large Structures]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
	[[Category: Cushman, M]]		[[Category: Cushman, M]]

OCA at 21:25, 24 January 2018

OCA — Wed, 24 Jan 2018 21:25:08 GMT

←Older revision		Revision as of 21:25, 24 January 2018
Line 1:		Line 1:
		+
	==Mutant Enzyme L119F Lumazine Synthase from S.pombe==		==Mutant Enzyme L119F Lumazine Synthase from S.pombe==
	<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://pdbe.org/1kz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://pdbe.org/1kz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kz9 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/kz/1kz9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kz/1kz9_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>

OCA at 02:40, 9 February 2016

OCA — Tue, 09 Feb 2016 02:40:01 GMT

←Older revision		Revision as of 02:40, 9 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=1kz9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:48, 10 September 2015

OCA — Thu, 10 Sep 2015 17:48:39 GMT

←Older revision		Revision as of 17:48, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Schizosaccharomyces_pombe Schizosaccharomyces pombe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://pdbe.org/1kz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 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 1kz9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]		[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
-	[[Category: ~~Schizosaccharomyces pombe~~]]	+	[[Category: Cbs 356]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
	[[Category: Cushman, M]]		[[Category: Cushman, M]]
Line 45:		Line 46:
	[[Category: Lumazine synthase]]		[[Category: Lumazine synthase]]
	[[Category: Riboflavin biosynthesis]]		[[Category: Riboflavin biosynthesis]]
		+	[[Category: Schizosaccharomyces pombe]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 03:50, 25 December 2014

OCA — Thu, 25 Dec 2014 03:50:44 GMT

←Older revision		Revision as of 03:50, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIB4_SCHPO RIB4_SCHPO]] 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. Also binds riboflavin with an unexpected high affinity.<ref>PMID:11856310</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]		[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
-	[[Category: Bacher, A.]]	+	[[Category: Bacher, A]]
-	[[Category: Cushman, M.]]	+	[[Category: Cushman, M]]
-	[[Category: Fischer, M.]]	+	[[Category: Fischer, M]]
-	[[Category: Gerhardt, S.]]	+	[[Category: Gerhardt, S]]
-	[[Category: Haase, I.]]	+	[[Category: Haase, I]]
-	[[Category: Huber, R.]]	+	[[Category: Huber, R]]
-	[[Category: Kaiser, J T.]]	+	[[Category: Kaiser, J T]]
-	[[Category: Steinbacher, S.]]	+	[[Category: Steinbacher, S]]
	[[Category: Ligand binding]]		[[Category: Ligand binding]]
	[[Category: Lumazine synthase]]		[[Category: Lumazine synthase]]
	[[Category: Riboflavin biosynthesis]]		[[Category: Riboflavin biosynthesis]]
-	[[Category: Schizosaccharomyces pombe]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 15:02, 29 September 2014

OCA — Mon, 29 Sep 2014 15:02:15 GMT

←Older revision		Revision as of 15:02, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kz9.~~png~~\|~~left~~\|200px]]	+	==Mutant Enzyme L119F Lumazine Synthase from S.pombe==
		+	<StructureSection load='1kz9' size='340' side='right' caption='[[1kz9]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kz9]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KZ9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kyv\|1kyv]], [[1kyx\|1kyx]], [[1kyy\|1kyy]], [[1kz1\|1kz1]], [[1kz4\|1kz4]], [[1kz6\|1kz6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6,7-dimethyl-8-ribityllumazine_synthase 6,7-dimethyl-8-ribityllumazine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.78 2.5.1.78] </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=1kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kz9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kz9 RCSB], [http://www.ebi.ac.uk/pdbsum/1kz9 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/kz/1kz9_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 ==
		+	Riboflavin is an essential cofactor in all organisms. Its direct biosynthetic precursor, 6,7-dimethyl-8-ribityllumazine, is synthesised by the enzyme 6,7-dimethyl-8-ribityllumazine synthase. Recently, we have found that the enzyme from Schizosaccharomyces pombe binds riboflavin, the final product of the pathway with a relatively high affinity with a KD of 1.2 microM. Here, we report on the crystal structure of lumazine synthase from S. pombe with bound riboflavin and compare the binding mode with those of the substrate analogue inhibitor 5-nitro-6-(D-ribitylamino)-2,4(1H,3H)-pyrimidinedione and of the product analogue 6-carboxyethyl-7-oxo-8-ribityllumazine. In all complexes the pyrimidinedione moieties of each respective ligand bind in a very similar orientation. Binding of riboflavin additionally involves a stacking interaction of the dimethylbenzene moiety with the side-chain of His94, a highly conserved residue in all lumazine synthases. The enzyme from Bacillus subtilis showed a KD of at least 1 mM whereas the very homologous enzyme from Saccharomyces cerevisiae had a comparable KD of 3.9 microM. Structural comparison of the S. cerevisiae, the S. pombe, and the mutant enzymes suggests that fine tuning of affinity is achieved by influencing this stacking interaction.

-	~~{{STRUCTURE_1kz9\| PDB=1kz9 \| SCENE= }}~~	+	The structural basis of riboflavin binding to Schizosaccharomyces pombe 6,7-dimethyl-8-ribityllumazine synthase.,Gerhardt S, Haase I, Steinbacher S, Kaiser JT, Cushman M, Bacher A, Huber R, Fischer M J Mol Biol. 2002 May 17;318(5):1317-29. PMID:12083520<ref>PMID:12083520</ref>

-	~~===Mutant Enzyme L119F Lumazine Synthase from S.pombe===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12083520}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1kz9]] is~~ a ~~5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KZ9 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012083520<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]		[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]

OCA at 12:02, 23 January 2013

OCA — Wed, 23 Jan 2013 12:02:43 GMT

←Older revision		Revision as of 12:02, 23 January 2013
Line 12:		Line 12:
	==Reference==		==Reference==
	<ref group="xtra">PMID:012083520</ref><references group="xtra"/>		<ref group="xtra">PMID:012083520</ref><references group="xtra"/>
-	[[Category: ~~Riboflavin~~ synthase]]	+	[[Category: 6,7-dimethyl-8-ribityllumazine synthase]]
	[[Category: Schizosaccharomyces pombe]]		[[Category: Schizosaccharomyces pombe]]
	[[Category: Bacher, A.]]		[[Category: Bacher, A.]]