1pwe - Revision history

OCA at 08:11, 14 February 2024

OCA — Wed, 14 Feb 2024 08:11:17 GMT

←Older revision		Revision as of 08:11, 14 February 2024
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	<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PWE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>~~[https://en.wikipedia.org/wiki/L~~-~~serine_ammonia-lyase L-serine ammonia-lyase]~~, ~~with EC number~~ [~~https://www~~.~~brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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]] 2.8Å</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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [https://pdbe.org/1pwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [https://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe 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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [https://pdbe.org/1pwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [https://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SDHL_RAT SDHL_RAT]
	== 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=1pwe 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=1pwe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent dehydration of L-serine to yield pyruvate and ammonia. Liver SDH plays an important role in gluconeogenesis. Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group of serine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatic hydrolysis to produce pyruvate. The crystal structure of rat liver apo-SDH was determined by single isomorphous replacement at 2.8 A resolution. The holo-SDH crystallized with O-methylserine (OMS) was also determined at 2.6 A resolution by molecular replacement. SDH is composed of two domains, and each domain has a typical alphabeta-open structure. The active site is located in the cleft between the two domains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can form the Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimer by inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed. Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization does not close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence ((168)GGGGL(172)) and forms hydrogen bonds with the amide groups of those amino acid residues, suggesting that the phosphate group can be protonated. N(1) of PLP participates in a hydrogen bond with Cys303, and similar hydrogen bonds with N(1) participating are seen in other beta-elimination enzymes. These hydrogen bonding schemes indicate that N(1) is not protonated, and thus, the pyridine ring cannot take a quinone-like structure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by forming the resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalytic mechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a general acid to donate a proton to the leaving hydroxyl group of serine.
-
-	Crystal structure of serine dehydratase from rat liver.,Yamada T, Komoto J, Takata Y, Ogawa H, Pitot HC, Takusagawa F Biochemistry. 2003 Nov 11;42(44):12854-65. PMID:14596599<ref>PMID:14596599</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pwe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Deaminase 3D structures\|Deaminase 3D structures]]		*[[Deaminase 3D structures\|Deaminase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
-	[[Category: L-serine ammonia-lyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Komoto, J]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Ogawa, H]]	+	[[Category: Komoto J]]
-	[[Category: Takata, Y]]	+	[[Category: Ogawa H]]
-	[[Category: Takusagawa, F]]	+	[[Category: Takata Y]]
-	[[Category: Yamada, T]]	+	[[Category: Takusagawa F]]
-	~~[[Category: Apo enzyme]]~~	+	[[Category: Yamada T]]
-	~~[[Category: L-serine dehydratase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Rat liver~~]]	+

OCA at 09:35, 8 September 2021

OCA — Wed, 08 Sep 2021 09:35:35 GMT

←Older revision		Revision as of 09:35, 8 September 2021
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	<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PWE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [~~http~~://pdbe.org/1pwe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe 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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [https://pdbe.org/1pwe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [https://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 10:08, 27 November 2019

OCA — Wed, 27 Nov 2019 10:08:55 GMT

←Older revision		Revision as of 10:08, 27 November 2019
Line 1:		Line 1:

	==Rat Liver L-Serine Dehydratase Apo Enzyme==		==Rat Liver L-Serine Dehydratase Apo Enzyme==
-	<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1pwe' size='340' side='right'caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
Line 26:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1pwe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pwe" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 32:		Line 35:
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
	[[Category: L-serine ammonia-lyase]]		[[Category: L-serine ammonia-lyase]]
		+	[[Category: Large Structures]]
	[[Category: Komoto, J]]		[[Category: Komoto, J]]
	[[Category: Ogawa, H]]		[[Category: Ogawa, H]]

OCA at 08:09, 24 February 2018

OCA — Sat, 24 Feb 2018 08:09:32 GMT

←Older revision		Revision as of 08:09, 24 February 2018
Line 1:		Line 1:
		+
	==Rat Liver L-Serine Dehydratase Apo Enzyme==		==Rat Liver L-Serine Dehydratase Apo Enzyme==
	<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://pdbe.org/1pwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe 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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://pdbe.org/1pwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pwe 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/pw/1pwe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pw/1pwe_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 25:		Line 26:
	</div>		</div>
	<div class="pdbe-citations 1pwe" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1pwe" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Deaminase\|Deaminase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:22, 10 February 2016

OCA — Wed, 10 Feb 2016 06:22:10 GMT

←Older revision		Revision as of 06:22, 10 February 2016
Line 14:		Line 14:
	<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=1pwe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:13, 11 September 2015

OCA — Fri, 11 Sep 2015 06:13:40 GMT

←Older revision		Revision as of 06:13, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe 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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://pdbe.org/1pwe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 1pwe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
	[[Category: L-serine ammonia-lyase]]		[[Category: L-serine ammonia-lyase]]
-	[[Category: Rattus norvegicus]]
	[[Category: Komoto, J]]		[[Category: Komoto, J]]
	[[Category: Ogawa, H]]		[[Category: Ogawa, H]]

OCA at 07:04, 6 January 2015

OCA — Tue, 06 Jan 2015 07:04:55 GMT

←Older revision		Revision as of 07:04, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe 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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe 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 33:		Line 33:
	[[Category: L-serine ammonia-lyase]]		[[Category: L-serine ammonia-lyase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Komoto, J.]]	+	[[Category: Komoto, J]]
-	[[Category: Ogawa, H.]]	+	[[Category: Ogawa, H]]
-	[[Category: Takata, Y.]]	+	[[Category: Takata, Y]]
-	[[Category: Takusagawa, F.]]	+	[[Category: Takusagawa, F]]
-	[[Category: Yamada, T.]]	+	[[Category: Yamada, T]]
	[[Category: Apo enzyme]]		[[Category: Apo enzyme]]
	[[Category: L-serine dehydratase]]		[[Category: L-serine dehydratase]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Rat liver]]		[[Category: Rat liver]]

OCA at 21:03, 28 September 2014

OCA — Sun, 28 Sep 2014 21:03:18 GMT

←Older revision		Revision as of 21:03, 28 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1pwe.~~png\|left~~\|200px]]	+	==Rat Liver L-Serine Dehydratase Apo Enzyme==
		+	<StructureSection load='1pwe' size='340' side='right' caption='[[1pwe]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PWE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-serine_ammonia-lyase L-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.17 4.3.1.17] </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=1pwe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pwe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pwe RCSB], [http://www.ebi.ac.uk/pdbsum/1pwe 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/pw/1pwe_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 ==
		+	SDH (L-serine dehydratase, EC 4.3.1.17) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent dehydration of L-serine to yield pyruvate and ammonia. Liver SDH plays an important role in gluconeogenesis. Formation of pyruvate by SDH is a two-step reaction in which the hydroxyl group of serine is cleaved to produce aminoacrylate, and then the aminoacrylate is deaminated by nonenzymatic hydrolysis to produce pyruvate. The crystal structure of rat liver apo-SDH was determined by single isomorphous replacement at 2.8 A resolution. The holo-SDH crystallized with O-methylserine (OMS) was also determined at 2.6 A resolution by molecular replacement. SDH is composed of two domains, and each domain has a typical alphabeta-open structure. The active site is located in the cleft between the two domains. The holo-SDH contained PLP-OMS aldimine in the active site, indicating that OMS can form the Schiff base linkage with PLP, but the subsequent dehydration did not occur. Apo-SDH forms a dimer by inserting the small domain into the catalytic cleft of the partner subunit so that the active site is closed. Holo-SDH also forms a dimer by making contacts at the back of the clefts so that the dimerization does not close the catalytic cleft. The phosphate group of PLP is surrounded by a characteristic G-rich sequence ((168)GGGGL(172)) and forms hydrogen bonds with the amide groups of those amino acid residues, suggesting that the phosphate group can be protonated. N(1) of PLP participates in a hydrogen bond with Cys303, and similar hydrogen bonds with N(1) participating are seen in other beta-elimination enzymes. These hydrogen bonding schemes indicate that N(1) is not protonated, and thus, the pyridine ring cannot take a quinone-like structure. These characteristics of the bound PLP suggest that SDH catalysis is not facilitated by forming the resonance-stabilized structure of the PLP-Ser aldimine as seen in aminotransferases. A possible catalytic mechanism involves the phosphate group, surrounded by the characteristic sequence, acting as a general acid to donate a proton to the leaving hydroxyl group of serine.

-	~~{{STRUCTURE_1pwe\| PDB=1pwe \| SCENE= }}~~	+	Crystal structure of serine dehydratase from rat liver.,Yamada T, Komoto J, Takata Y, Ogawa H, Pitot HC, Takusagawa F Biochemistry. 2003 Nov 11;42(44):12854-65. PMID:14596599<ref>PMID:14596599</ref>

-	~~===Rat Liver L-Serine Dehydratase Apo Enzyme===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_14596599}}~~	+	==See Also==
-		+	*[[Deaminase\|Deaminase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1pwe~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:014596599<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: L-serine ammonia-lyase]]		[[Category: L-serine ammonia-lyase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

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

OCA — Wed, 19 Dec 2012 12:11:30 GMT

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

←Older revision

Revision as of 12:11, 19 December 2012

OCA at 12:11, 19 December 2012

OCA — Wed, 19 Dec 2012 12:11:27 GMT

←Older revision		Revision as of 12:11, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pwe.png\|left\|200px]]		[[Image:1pwe.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pwe", 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_1pwe\| PDB=1pwe \| SCENE= }}		{{STRUCTURE_1pwe\| PDB=1pwe \| SCENE= }}

	===Rat Liver L-Serine Dehydratase Apo Enzyme===		===Rat Liver L-Serine Dehydratase Apo Enzyme===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14596599}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14596599 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14596599}}		{{ABSTRACT_PUBMED_14596599}}

	==About this Structure==		==About this Structure==
-	~~1PWE~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA].	+	[[1pwe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PWE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14596599~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014596599</ref><references group="xtra"/>
	[[Category: L-serine ammonia-lyase]]		[[Category: L-serine ammonia-lyase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
Line 33:		Line 21:
	[[Category: Apo enzyme]]		[[Category: Apo enzyme]]
	[[Category: L-serine dehydratase]]		[[Category: L-serine dehydratase]]
		+	[[Category: Lyase]]
	[[Category: Rat liver]]		[[Category: Rat liver]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:06:13 2009''