1sjc - Revision history

OCA at 08:31, 14 February 2024

2024-02-14T08:31:16Z

←Older revision		Revision as of 08:31, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1sjc' size='340' side='right'caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1sjc' size='340' side='right'caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1SJC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJC FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])~~</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [https://pdbe.org/1sjc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [https://www.ebi.ac.uk/pdbsum/1sjc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjc ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [~~http~~://pdbe.org/1sjc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1sjc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjc ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NSAR_AMYSP NSAR_AMYSP] Acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-phenylglycine and N-succinyl-methionine (PubMed:14705949, PubMed:24955846). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl-D/L-methionine, N-propionyl-D/L-methionine, N-butyryl-D/L-methionine and N-chloroacetyl-L-valine (PubMed:7766084, PubMed:10194342, PubMed:14705949, PubMed:23130969). Also converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:10194342, PubMed:14705949, PubMed:24955846). Catalyzes both N-succinylamino acid racemization and OSB synthesis at equivalent rates (PubMed:14705949, PubMed:24955846). NSAR is probably the biological function of this enzyme (Probable).<ref>PMID:10194342</ref> <ref>PMID:14705949</ref> <ref>PMID:23130969</ref> <ref>PMID:24955846</ref> <ref>PMID:7766084</ref> <ref>PMID:16740275</ref> <ref>PMID:24955846</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1sjc 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=1sjc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.
-
-	Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.,Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I Biochemistry. 2004 May 18;43(19):5716-27. PMID:15134446<ref>PMID:15134446</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1sjc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	[[Category: Amycolatopsis sp]]		[[Category: Amycolatopsis sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garrett~~, J B~~]]	+	[[Category: Garrett JB]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Rayment, I]]	+	[[Category: Rayment I]]
-	[[Category: Taylor-Ringia~~, E A~~]]	+	[[Category: Taylor-Ringia EA]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Racemase~~]]	+

OCA at 11:27, 24 December 2020

2020-12-24T11:27:39Z

←Older revision		Revision as of 11:27, 24 December 2020
Line 1:		Line 1:

	==x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine==		==x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine==
-	<StructureSection load='1sjc' size='340' side='right' caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1sjc' size='340' side='right'caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1SJC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1SJC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://pdbe.org/1sjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjc ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://pdbe.org/1sjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Amycolatopsis sp]]		[[Category: Amycolatopsis sp]]
		+	[[Category: Large Structures]]
	[[Category: Garrett, J B]]		[[Category: Garrett, J B]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]

OCA at 07:41, 14 March 2018

2018-03-14T07:41:32Z

←Older revision		Revision as of 07:41, 14 March 2018
Line 1:		Line 1:
		+
	==x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine==		==x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine==
	<StructureSection load='1sjc' size='340' side='right' caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1sjc' size='340' side='right' caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://pdbe.org/1sjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc 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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://pdbe.org/1sjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sjc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sjc_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 04:39, 10 February 2016

2016-02-10T04:39:41Z

←Older revision		Revision as of 04:39, 10 February 2016
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	<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=1sjc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:28, 11 September 2015

2015-09-11T05:28:05Z

←Older revision		Revision as of 05:28, 11 September 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc 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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://pdbe.org/1sjc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc PDBsum]</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 1sjc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:00, 6 January 2015

2015-01-06T08:00:13Z

←Older revision		Revision as of 08:00, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJC FirstGlance]. <br>		<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc 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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Amycolatopsis sp.]]	+	[[Category: Amycolatopsis sp]]
-	[[Category: Garrett, J B.]]	+	[[Category: Garrett, J B]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
-	[[Category: Rayment, I.]]	+	[[Category: Rayment, I]]
-	[[Category: Taylor-Ringia, E A.]]	+	[[Category: Taylor-Ringia, E A]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Racemase]]		[[Category: Racemase]]

OCA at 14:34, 29 September 2014

2014-09-29T14:34:12Z

←Older revision		Revision as of 14:34, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1sjc.~~png~~\|~~left~~\|200px]]	+	==x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine==
		+	<StructureSection load='1sjc' size='340' side='right' caption='[[1sjc]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SJC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SMG:N-SUCCINYL+METHIONINE'>SMG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1sja\|1sja]], [[1sjb\|1sjb]], [[1sjd\|1sjd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AAAR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37632 Amycolatopsis sp.])</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=1sjc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1sjc RCSB], [http://www.ebi.ac.uk/pdbsum/1sjc 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/sj/1sjc_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 ==
		+	Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.

-	~~{{STRUCTURE_1sjc\| PDB=1sjc \| SCENE= }}~~	+	Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis.,Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I Biochemistry. 2004 May 18;43(19):5716-27. PMID:15134446<ref>PMID:15134446</ref>

-	~~===x-ray structure~~ of ~~o-succinylbenzoate synthase complexed with N-succinyl methionine===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15134446}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1sjc]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Amycolatopsis_sp~~. ~~Amycolatopsis sp.]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015134446<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Amycolatopsis sp.]]		[[Category: Amycolatopsis sp.]]
	[[Category: Garrett, J B.]]		[[Category: Garrett, J B.]]

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

2013-01-04T10:20:32Z

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

←Older revision

Revision as of 10:20, 4 January 2013

OCA at 10:20, 4 January 2013

2013-01-04T10:20:29Z

←Older revision		Revision as of 10:20, 4 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1sjc.png\|left\|200px]]		[[Image:1sjc.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1sjc", 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_1sjc\| PDB=1sjc \| SCENE= }}		{{STRUCTURE_1sjc\| PDB=1sjc \| SCENE= }}

	===x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine===		===x-ray structure of o-succinylbenzoate synthase complexed with N-succinyl methionine===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15134446}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15134446 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15134446}}		{{ABSTRACT_PUBMED_15134446}}

	==About this Structure==		==About this Structure==
-	~~1SJC~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA].	+	[[1sjc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15134446~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015134446</ref><references group="xtra"/>
	[[Category: Amycolatopsis sp.]]		[[Category: Amycolatopsis sp.]]
	[[Category: Garrett, J B.]]		[[Category: Garrett, J B.]]
Line 31:		Line 19:
	[[Category: Taylor-Ringia, E A.]]		[[Category: Taylor-Ringia, E A.]]
	[[Category: Thoden, J B.]]		[[Category: Thoden, J B.]]
		+	[[Category: Isomerase]]
		+	[[Category: Lyase]]
	[[Category: Racemase]]		[[Category: Racemase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:30:11 2009''

OCA at 13:30, 17 February 2009

2009-02-17T13:30:13Z

←Older revision		Revision as of 13:30, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1SJC is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA].	+	1SJC is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJC OCA].

	==Reference==		==Reference==
-	Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis., Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I, Biochemistry. 2004 May 18;43(19):5716-27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15134446 15134446]~~	+	<ref group="xtra">PMID:15134446</ref><references group="xtra"/>
	[[Category: Amycolatopsis sp.]]		[[Category: Amycolatopsis sp.]]
-	[[Category: Single protein]]
	[[Category: Garrett, J B.]]		[[Category: Garrett, J B.]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]
Line 34:		Line 33:
	[[Category: Racemase]]		[[Category: Racemase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 21:10~~:30 ~~2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:30:11 2009''