2ola - Revision history

OCA at 10:42, 30 August 2023

OCA — Wed, 30 Aug 2023 10:42:11 GMT

←Older revision		Revision as of 10:42, 30 August 2023
Line 1:		Line 1:

	==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==		==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==
-	<StructureSection load='2ola' size='340' side='right'caption='[[2ola]]' scene=''>	+	<StructureSection load='2ola' size='340' side='right'caption='[[2ola]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OLA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ola]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_COL Staphylococcus aureus subsp. aureus COL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OLA FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [https://pdbe.org/2ola PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [https://www.ebi.ac.uk/pdbsum/2ola PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ola ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></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]] 2.45Å</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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [https://pdbe.org/2ola PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [https://www.ebi.ac.uk/pdbsum/2ola PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ola ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H3KH80_STAAE A0A0H3KH80_STAAE] Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB).[HAMAP-Rule:MF_01933]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ola 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=2ola ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions.
		+
		+	Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.,Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME Proc Natl Acad Sci U S A. 2014 May 28. pii: 201318703. PMID:24872444<ref>PMID:24872444</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 2ola" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Staphylococcus aureus subsp. aureus COL]]
	[[Category: Almo SC]]		[[Category: Almo SC]]
	[[Category: Burley SK]]		[[Category: Burley SK]]

OCA at 12:59, 9 June 2021

OCA — Wed, 09 Jun 2021 12:59:28 GMT

←Older revision		Revision as of 12:59, 9 June 2021
Line 1:		Line 1:

	==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==		==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==
-	<StructureSection load='2ola' size='340' side='right' caption='[[2ola]]~~, [[Resolution\|resolution]] 2.45Å~~' scene=''>	+	<StructureSection load='2ola' size='340' side='right'caption='[[2ola]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[2ola]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OLA FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OLA FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2okt\|2okt]]</td></tr>~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [https://pdbe.org/2ola PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [https://www.ebi.ac.uk/pdbsum/2ola PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ola ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [~~http~~://pdbe.org/2ola PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ola PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ola ProSAT], [~~http~~://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 19:		Line 16:
	</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=2ola 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=2ola ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions.
-
-	Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.,Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME Proc Natl Acad Sci U S A. 2014 May 28. pii: 201318703. PMID:24872444<ref>PMID:24872444</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ola" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Staac]]~~	+	[[Category: Large Structures]]
-	~~[[Category: O-succinylbenzoate--CoA ligase~~]]	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Burley SK]]
-	[[Category: Burley~~, S K~~]]	+	[[Category: Dickey M]]
-	[[Category: Dickey, M]]	+	[[Category: Gerlt JA]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gheyi T]]
-	[[Category: Gheyi, T]]	+	[[Category: Maletic M]]
-	[[Category: Maletic, M]]	+	[[Category: Ozyurt S]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Patskovsky Y]]
-	[[Category: Ozyurt, S]]	+	[[Category: Reyes C]]
-	[[Category: Patskovsky, Y]]	+	[[Category: Sauder JM]]
-	[[Category: Reyes, C]]	+	[[Category: Smith D]]
-	[[Category: Sauder~~, J M~~]]	+	[[Category: Wasserman SR]]
-	[[Category: Smith, D]]	+
-	[[Category: Wasserman~~, S R]]~~	+
-	~~[[Category: Enolase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: O-succinylbenzoic acid synthetase]]~~	+
-	~~[[Category: PSI, Protein structure initiative~~]]	+

OCA at 08:28, 14 November 2018

OCA — Wed, 14 Nov 2018 08:28:50 GMT

←Older revision		Revision as of 08:28, 14 November 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ol/2ola_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ol/2ola_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 09:02, 18 October 2017

OCA — Wed, 18 Oct 2017 09:02:58 GMT

←Older revision		Revision as of 09:02, 18 October 2017
Line 1:		Line 1:
		+
	==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==		==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==
	<StructureSection load='2ola' size='340' side='right' caption='[[2ola]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='2ola' size='340' side='right' caption='[[2ola]], [[Resolution\|resolution]] 2.45Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://pdbe.org/2ola PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://pdbe.org/2ola PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ola ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 16:27, 7 February 2016

OCA — Sun, 07 Feb 2016 16:27:33 GMT

←Older revision		Revision as of 16:27, 7 February 2016
Line 16:		Line 16:
	<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=2ola ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:14, 10 September 2015

OCA — Thu, 10 Sep 2015 03:14:07 GMT

←Older revision		Revision as of 03:14, 10 September 2015
Line 6:		Line 6:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://pdbe.org/2ola PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2ola" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:18, 6 November 2014

OCA — Thu, 06 Nov 2014 13:18:26 GMT

←Older revision		Revision as of 13:18, 6 November 2014
Line 32:		Line 32:
	[[Category: Staac]]		[[Category: Staac]]
	[[Category: O-succinylbenzoate--CoA ligase]]		[[Category: O-succinylbenzoate--CoA ligase]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: Dickey, M.]]	+	[[Category: Dickey, M]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Gheyi, T.]]	+	[[Category: Gheyi, T]]
-	[[Category: Maletic, M.]]	+	[[Category: Maletic, M]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Ozyurt, S.]]	+	[[Category: Ozyurt, S]]
-	[[Category: Patskovsky, Y.]]	+	[[Category: Patskovsky, Y]]
-	[[Category: Reyes, C.]]	+	[[Category: Reyes, C]]
-	[[Category: Sauder, J M.]]	+	[[Category: Sauder, J M]]
-	[[Category: Smith, D.]]	+	[[Category: Smith, D]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Wasserman, S R]]
	[[Category: Enolase]]		[[Category: Enolase]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: New york sgx research center for structural genomic]]
-	[[Category: New york structural genomics research consortium]]
	[[Category: Nysgrc]]		[[Category: Nysgrc]]
-	[[Category: ~~Nysgxrc~~]]	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
	[[Category: O-succinylbenzoic acid synthetase]]		[[Category: O-succinylbenzoic acid synthetase]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+

OCA at 06:28, 10 October 2014

OCA — Fri, 10 Oct 2014 06:28:48 GMT

←Older revision		Revision as of 06:28, 10 October 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ola]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OLA FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ola]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OLA FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2okt\|2okt]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2okt\|2okt]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:51, 11 June 2014

OCA — Wed, 11 Jun 2014 06:51:18 GMT

←Older revision		Revision as of 06:51, 11 June 2014
Line 1:		Line 1:
-	[[~~Image:~~2ola.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form==
		+	<StructureSection load='2ola' size='340' side='right' caption='[[2ola]], [[Resolution\|resolution]] 2.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ola]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Staac Staac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OLA FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2okt\|2okt]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">menc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=93062 STAAC])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/o-succinylbenzoate--CoA_ligase o-succinylbenzoate--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.26 6.2.1.26] </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=2ola FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ola OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ola RCSB], [http://www.ebi.ac.uk/pdbsum/2ola PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2ola TOPSAN]</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/ol/2ola_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 rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. Determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. As a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (OSBS) family, which catalyzes a step in menaquinone synthesis in diverse microorganisms and plants. On average, the OSBS family is much more divergent than other protein families from the same set of species, with the most divergent family members sharing <15% sequence identity. Comparing 11 representative structures revealed that loss of quaternary structure and large deletions or insertions are associated with the family's rapid evolution. Neither of these properties has been investigated in previous studies to identify factors that affect the rate of protein evolution. Intriguingly, one subfamily retained a multimeric quaternary structure and has small insertions and deletions compared with related enzymes that catalyze diverse reactions. Many proteins in this subfamily catalyze both OSBS and N-succinylamino acid racemization (NSAR). Retention of ancestral structural characteristics in the NSAR/OSBS subfamily suggests that the rate of protein evolution is not proportional to the capacity to evolve new protein functions. Instead, structural features that are conserved among proteins with diverse functions might contribute to the evolution of new functions.

-	~~{{STRUCTURE_2ola\| PDB=2ola \| SCENE= }}~~	+	Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.,Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME Proc Natl Acad Sci U S A. 2014 May 28. pii: 201318703. PMID:24872444<ref>PMID:24872444</ref>

-	~~===Crystal structure~~ of ~~O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	==~~About this Structure~~==	+	<references/>
-	~~[[2ola]] is a 1 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_col Staphylococcus aureus subsp. aureus col]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OLA OCA].	+	__TOC__
-	[[Category: ~~Staphylococcus aureus subsp. aureus col~~]]	+	</StructureSection>
		+	[[Category: Staac]]
	[[Category: O-succinylbenzoate--CoA ligase]]		[[Category: O-succinylbenzoate--CoA ligase]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA: Protected "2ola" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 14:55:49 GMT

Protected "2ola" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:55, 7 January 2013