1m4s - Revision history

OCA at 08:31, 10 April 2024

OCA — Wed, 10 Apr 2024 08:31:35 GMT

←Older revision		Revision as of 08:31, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1m4s' size='340' side='right'caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='1m4s' size='340' side='right'caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_19544 Atcc 19544~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.87Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SCY~~:~~S-ACETYL-CYSTEINE~~'>~~SCY~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;~~'>~~[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [https://pdbe.org/1m4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [https://www.ebi.ac.uk/pdbsum/1m4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4s 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=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [https://pdbe.org/1m4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [https://www.ebi.ac.uk/pdbsum/1m4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4s ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/THIL_SHIZO THIL_SHIZO]
	== 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=1m4s 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=1m4s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Biosynthetic thiolase catalyzes the formation of acetoacetyl-CoA from two molecules of acetyl-CoA. This is a key step in the synthesis of many biological compounds, including steroid hormones and ketone bodies. The thiolase reaction involves two chemically distinct steps; during acyl transfer, an acetyl group is transferred from acetyl-CoA to Cys89, and in the Claisen condensation step, this acetyl group is further transferred to a second molecule of acetyl-CoA, generating acetoacetyl-CoA. Here, new crystallographic data for Zoogloea ramigera biosynthetic thiolase are presented, covering all intermediates of the thiolase catalytic cycle. The high-resolution structures indicate that the acetyl group goes through four conformations while being transferred from acetyl-CoA via the acetylated enzyme to acetoacetyl-CoA. This transfer is catalyzed in a rigid cavity lined by mostly hydrophobic side chains, in addition to the catalytic residues Cys89, His348, and Cys378. The structures highlight the importance of an oxyanion hole formed by a water molecule and His348 in stabilizing the negative charge on the thioester oxygen atom of acetyl-CoA at two different steps of the reaction cycle. Another oxyanion hole, composed of the main chain nitrogen atoms of Cys89 and Gly380, complements a negative charge of the thioester oxygen anion of the acetylated intermediate, stabilizing the tetrahedral transition state of the Claisen condensation step. The reactivity of the active site may be modulated by hydrogen bonding networks extending from the active site toward the back of the molecule.
-
-	The catalytic cycle of biosynthetic thiolase: a conformational journey of an acetyl group through four binding modes and two oxyanion holes.,Kursula P, Ojala J, Lambeir AM, Wierenga RK Biochemistry. 2002 Dec 31;41(52):15543-56. PMID:12501183<ref>PMID:12501183</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1m4s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Thiolase 3D structures\|Thiolase 3D structures]]		*[[Thiolase 3D structures\|Thiolase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Acetyl-CoA C-acetyltransferase]]
-	[[Category: Atcc 19544]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kursula, P]]	+	[[Category: Zoogloea ramigera]]
-	[[Category: Lambeir, A M]]	+	[[Category: Kursula P]]
-	[[Category: Ojala, J]]	+	[[Category: Lambeir A-M]]
-	[[Category: Wierenga~~, R K]]~~	+	[[Category: Ojala J]]
-	~~[[Category: Acetylated intermediate]]~~	+	[[Category: Wierenga RK]]
-	~~[[Category: Thiolase fold]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 09:52, 15 September 2021

OCA — Wed, 15 Sep 2021 09:52:17 GMT

←Older revision		Revision as of 09:52, 15 September 2021
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	<StructureSection load='1m4s' size='340' side='right'caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='1m4s' size='340' side='right'caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1M4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [~~http~~://pdbe.org/1m4s PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1m4s PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4s 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=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [https://pdbe.org/1m4s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [https://www.ebi.ac.uk/pdbsum/1m4s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4s ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Thiolase\|Thiolase]]	+	*[[Thiolase 3D structures\|Thiolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:33, 11 December 2019

OCA — Wed, 11 Dec 2019 19:33:58 GMT

←Older revision		Revision as of 19:33, 11 December 2019
Line 1:		Line 1:

	==Biosynthetic thiolase, Cys89 acetylated, unliganded form==		==Biosynthetic thiolase, Cys89 acetylated, unliganded form==
-	<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>	+	<StructureSection load='1m4s' size='340' side='right'caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
Line 38:		Line 38:
	[[Category: Acetyl-CoA C-acetyltransferase]]		[[Category: Acetyl-CoA C-acetyltransferase]]
	[[Category: Atcc 19544]]		[[Category: Atcc 19544]]
		+	[[Category: Large Structures]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]
	[[Category: Lambeir, A M]]		[[Category: Lambeir, A M]]

OCA at 05:27, 8 March 2018

OCA — Thu, 08 Mar 2018 05:27:40 GMT

←Older revision		Revision as of 05:27, 8 March 2018
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1m4s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m4s" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thiolase\|Thiolase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:04, 31 January 2018

OCA — Wed, 31 Jan 2018 08:04:13 GMT

←Older revision		Revision as of 08:04, 31 January 2018
Line 1:		Line 1:
		+
	==Biosynthetic thiolase, Cys89 acetylated, unliganded form==		==Biosynthetic thiolase, Cys89 acetylated, unliganded form==
	<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://pdbe.org/1m4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s 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=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://pdbe.org/1m4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m4s ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m4/1m4s_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m4/1m4s_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1m4s" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1m4s" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thiolase\|Thiolase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:26, 10 February 2016

OCA — Wed, 10 Feb 2016 03:26:46 GMT

←Older revision		Revision as of 03:26, 10 February 2016
Line 17:		Line 17:
	<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=1m4s ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:54, 11 September 2015

OCA — Fri, 11 Sep 2015 04:54:50 GMT

←Older revision		Revision as of 04:54, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>		<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Zoogloea_ramigera Zoogloea ramigera~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19544 Atcc 19544]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s 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=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://pdbe.org/1m4s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 27:		Line 27:
	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 1m4s" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Acetyl-CoA C-acetyltransferase]]		[[Category: Acetyl-CoA C-acetyltransferase]]
-	[[Category: ~~Zoogloea ramigera~~]]	+	[[Category: Atcc 19544]]
	[[Category: Kursula, P]]		[[Category: Kursula, P]]
	[[Category: Lambeir, A M]]		[[Category: Lambeir, A M]]

OCA at 15:58, 5 January 2015

OCA — Mon, 05 Jan 2015 15:58:04 GMT

←Older revision		Revision as of 15:58, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>		<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s 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=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s 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 36:		Line 36:
	[[Category: Acetyl-CoA C-acetyltransferase]]		[[Category: Acetyl-CoA C-acetyltransferase]]
	[[Category: Zoogloea ramigera]]		[[Category: Zoogloea ramigera]]
-	[[Category: Kursula, P.]]	+	[[Category: Kursula, P]]
-	[[Category: Lambeir, A M.]]	+	[[Category: Lambeir, A M]]
-	[[Category: Ojala, J.]]	+	[[Category: Ojala, J]]
-	[[Category: Wierenga, R K.]]	+	[[Category: Wierenga, R K]]
	[[Category: Acetylated intermediate]]		[[Category: Acetylated intermediate]]
	[[Category: Thiolase fold]]		[[Category: Thiolase fold]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 13:25, 28 September 2014

OCA — Sun, 28 Sep 2014 13:25:05 GMT

←Older revision		Revision as of 13:25, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1m4s.~~png~~\|~~left~~\|200px]]	+	==Biosynthetic thiolase, Cys89 acetylated, unliganded form==
		+	<StructureSection load='1m4s' size='340' side='right' caption='[[1m4s]], [[Resolution\|resolution]] 1.87Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M4S FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCY:S-ACETYL-CYSTEINE'>SCY</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dlu\|1dlu]], [[1dlv\|1dlv]], [[1qfl\|1qfl]], [[1dm3\|1dm3]], [[1m1o\|1m1o]], [[1m1t\|1m1t]], [[1m3z\|1m3z]], [[1m4t\|1m4t]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acetyltransferase Acetyl-CoA C-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.9 2.3.1.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m4s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m4s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1m4s RCSB], [http://www.ebi.ac.uk/pdbsum/1m4s 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/m4/1m4s_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 ==
		+	Biosynthetic thiolase catalyzes the formation of acetoacetyl-CoA from two molecules of acetyl-CoA. This is a key step in the synthesis of many biological compounds, including steroid hormones and ketone bodies. The thiolase reaction involves two chemically distinct steps; during acyl transfer, an acetyl group is transferred from acetyl-CoA to Cys89, and in the Claisen condensation step, this acetyl group is further transferred to a second molecule of acetyl-CoA, generating acetoacetyl-CoA. Here, new crystallographic data for Zoogloea ramigera biosynthetic thiolase are presented, covering all intermediates of the thiolase catalytic cycle. The high-resolution structures indicate that the acetyl group goes through four conformations while being transferred from acetyl-CoA via the acetylated enzyme to acetoacetyl-CoA. This transfer is catalyzed in a rigid cavity lined by mostly hydrophobic side chains, in addition to the catalytic residues Cys89, His348, and Cys378. The structures highlight the importance of an oxyanion hole formed by a water molecule and His348 in stabilizing the negative charge on the thioester oxygen atom of acetyl-CoA at two different steps of the reaction cycle. Another oxyanion hole, composed of the main chain nitrogen atoms of Cys89 and Gly380, complements a negative charge of the thioester oxygen anion of the acetylated intermediate, stabilizing the tetrahedral transition state of the Claisen condensation step. The reactivity of the active site may be modulated by hydrogen bonding networks extending from the active site toward the back of the molecule.

-	~~{{STRUCTURE_1m4s\| PDB=1m4s \| SCENE= }}~~	+	The catalytic cycle of biosynthetic thiolase: a conformational journey of an acetyl group through four binding modes and two oxyanion holes.,Kursula P, Ojala J, Lambeir AM, Wierenga RK Biochemistry. 2002 Dec 31;41(52):15543-56. PMID:12501183<ref>PMID:12501183</ref>

-	~~===Biosynthetic thiolase~~, ~~Cys89 acetylated, unliganded form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12501183}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1m4s]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Zoogloea_ramigera Zoogloea ramigera]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA].~~	+

	==See Also==		==See Also==
	*[[Thiolase\|Thiolase]]		*[[Thiolase\|Thiolase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012501183<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Acetyl-CoA C-acetyltransferase]]		[[Category: Acetyl-CoA C-acetyltransferase]]
	[[Category: Zoogloea ramigera]]		[[Category: Zoogloea ramigera]]

OCA at 16:10, 20 October 2012

OCA — Sat, 20 Oct 2012 16:10:15 GMT

←Older revision		Revision as of 16:10, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1m4s]] is a 4 chain structure ~~of [[Thiolase]]~~ with sequence from [http://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA].	+	[[1m4s]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Zoogloea_ramigera Zoogloea ramigera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M4S OCA].

	==See Also==		==See Also==