3r0z - Revision history

OCA at 08:35, 20 March 2024

OCA — Wed, 20 Mar 2024 08:35:38 GMT

←Older revision		Revision as of 08:35, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3r0z' size='340' side='right'caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3r0z' size='340' side='right'caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3r0x\|3r0x]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dsdA, STM3802 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~90371~~ "~~Bacillus typhimurium~~" ~~Loeffler 1892])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18]~~ </~~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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [https://pdbe.org/3r0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [https://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z 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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [https://pdbe.org/3r0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [https://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/SDHD_SALTY SDHD_SALTY]
-	Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-Serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggests that Thr 166 may be involved in abstraction of proton from the Calpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses alpha, beta elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.	+
-		+
-	Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis.,Bharath SR, Bisht S, Savithri HS, Murthy MR FEBS J. 2011 Jun 10. doi: ~~10.1111~~/~~j.1742-4658.2011.08210.x. PMID:21668644<ref>PMID:21668644<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3r0z" 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: Bacillus typhimurium loeffler 1892]]
-	[[Category: D-serine ammonia-lyase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Bharath, S R]]~~	+	[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
-	~~[[Category: Murthy, M R~~.N]]	+	[[Category: Bharath SR]]
-	[[Category: ~~Savithri, H S~~]]	+	[[Category: Murthy MRN]]
-	[[Category: ~~Shveta, B~~]]	+	[[Category: Savithri HS]]
-	[[Category: ~~Alpha~~]]	+	[[Category: Shveta B]]
-	[[Category: ~~Beta elimination of d-serine]]~~	+
-	~~[[Category: Foldtype 2 family of plp-dependent enzyme]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 05:44, 15 June 2022

OCA — Wed, 15 Jun 2022 05:44:27 GMT

←Older revision		Revision as of 05:44, 15 June 2022
Line 1:		Line 1:

	==Crystal structure of apo D-serine deaminase from Salmonella typhimurium==		==Crystal structure of apo D-serine deaminase from Salmonella typhimurium==
-	<StructureSection load='3r0z' size='340' side='right' caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='3r0z' size='340' side='right'caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</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">[[3r0x\|3r0x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r0x\|3r0x]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [~~http~~://pdbe.org/3r0z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z 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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [https://pdbe.org/3r0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [https://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Deaminase\|Deaminase]]	+	*[[Deaminase 3D structures\|Deaminase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 28:		Line 28:
	[[Category: Bacillus typhimurium loeffler 1892]]		[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: D-serine ammonia-lyase]]		[[Category: D-serine ammonia-lyase]]
		+	[[Category: Large Structures]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Murthy, M R.N]]		[[Category: Murthy, M R.N]]

OCA at 08:25, 4 August 2016

OCA — Thu, 04 Aug 2016 08:25:21 GMT

←Older revision		Revision as of 08:25, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of apo D-serine deaminase from Salmonella typhimurium==		==Crystal structure of apo D-serine deaminase from Salmonella typhimurium==
	<StructureSection load='3r0z' size='340' side='right' caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='3r0z' size='340' side='right' caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar~~ typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_typhimurium"_loeffler_1892 "bacillus typhimurium" loeffler 1892]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=EDO:1,2-ETHANEDIOL'>EDO</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">[[3r0x\|3r0x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r0x\|3r0x]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 ~~Salmonella enterica subsp. enterica serovar Typhimurium~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 "Bacillus typhimurium" Loeffler 1892])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [http://www.ebi.ac.uk/pdbsum/3r0z 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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [http://pdbe.org/3r0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [http://www.ebi.ac.uk/pdbsum/3r0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r0z ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3r0z" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus typhimurium loeffler 1892]]
	[[Category: D-serine ammonia-lyase]]		[[Category: D-serine ammonia-lyase]]
-	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
	[[Category: Bharath, S R]]		[[Category: Bharath, S R]]
	[[Category: Murthy, M R.N]]		[[Category: Murthy, M R.N]]

OCA at 11:11, 19 December 2014

OCA — Fri, 19 Dec 2014 11:11:41 GMT

←Older revision		Revision as of 11:11, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3r0z\| PDB=3r0z \| SCENE= }}~~	+	==Crystal structure of apo D-serine deaminase from Salmonella typhimurium==
-	===Crystal structure of apo D-serine deaminase from Salmonella typhimurium===	+	<StructureSection load='3r0z' size='340' side='right' caption='[[3r0z]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21668644}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3r0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R0Z FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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">[[3r0x\|3r0x]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dsdA, STM3802 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D-serine_ammonia-lyase D-serine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.18 4.3.1.18] </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=3r0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r0z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r0z RCSB], [http://www.ebi.ac.uk/pdbsum/3r0z PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Metabolism of D-amino acids is of considerable interest due to their key importance in cell structure and function. Salmonella typhimurium D-Serine deaminase (StDSD) is a pyridoxal 5' phosphate (PLP)-dependent enzyme that catalyzes degradation of D-Ser to pyruvate and ammonia. The first crystal structure of D-serine deaminase described here reveals a typical Foldtype II or tryptophan synthase beta subunit fold of PLP-dependent enzymes. Although holoenzyme was used for crystallization of both wild type StDSD (WtDSD) and selenomethionine labelled StDSD (SeMetDSD), significant electron density was not observed for the co-factor, indicating that the enzyme has a low affinity for the cofactor under crystallization conditions. Interestingly, unexpected conformational differences were observed between the two structures. The WtDSD was in an open conformation while SeMetDSD, crystallized in the presence of isoserine, was in a closed conformation suggesting that the enzyme is likely to undergo conformational changes upon binding of substrate as observed in other Foldtype II PLP-dependent enzymes. Electron density corresponding to a plausible sodium ion was found near the active site of the closed but not in the open state of the enzyme. Examination of the active site and substrate modeling suggests that Thr 166 may be involved in abstraction of proton from the Calpha atom of the substrate. Apart from the physiological reaction, StDSD catalyses alpha, beta elimination of D-Thr, D-Allothr and L-Ser to the corresponding alpha-keto acids and ammonia. The structure of StDSD provides a molecular framework necessary for understanding differences in the rate of reaction with these substrates.

-	~~==About this Structure==~~	+	Crystal structures of open and closed forms of D-serine deaminase from Salmonella typhimurium - implications on substrate specificity and catalysis.,Bharath SR, Bisht S, Savithri HS, Murthy MR FEBS J. 2011 Jun 10. doi: 10.1111/j.1742-4658.2011.08210.x. PMID:21668644<ref>PMID:21668644</ref>
-	~~[[3r0z]] is a 1 chain structure with sequence~~ from ~~[http~~:/~~/en~~.~~wikipedia~~.~~org/wiki/Salmonella_enterica_subsp~~.~~_enterica_serovar_typhimurium Salmonella enterica subsp~~. ~~enterica serovar typhimurium]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:021668644</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Deaminase\|Deaminase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: D-serine ammonia-lyase]]		[[Category: D-serine ammonia-lyase]]
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
-	[[Category: Bharath, S R.]]	+	[[Category: Bharath, S R]]
-	[[Category: Murthy, M R.N.]]	+	[[Category: Murthy, M R.N]]
-	[[Category: Savithri, H S.]]	+	[[Category: Savithri, H S]]
-	[[Category: Shveta, B.]]	+	[[Category: Shveta, B]]
	[[Category: Alpha]]		[[Category: Alpha]]
	[[Category: Beta elimination of d-serine]]		[[Category: Beta elimination of d-serine]]
	[[Category: Foldtype 2 family of plp-dependent enzyme]]		[[Category: Foldtype 2 family of plp-dependent enzyme]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 08:12, 16 May 2013

OCA — Thu, 16 May 2013 08:12:09 GMT

←Older revision		Revision as of 08:12, 16 May 2013
Line 1:		Line 1:
-	[[Image:3r0z.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3r0z", 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_3r0z\| PDB=3r0z \| SCENE= }}		{{STRUCTURE_3r0z\| PDB=3r0z \| SCENE= }}
-
	===Crystal structure of apo D-serine deaminase from Salmonella typhimurium===		===Crystal structure of apo D-serine deaminase from Salmonella typhimurium===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21668644}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21668644 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21668644}}		{{ABSTRACT_PUBMED_21668644}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021668644</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021668644</ref><references group="xtra"/><references/>
	[[Category: D-serine ammonia-lyase]]		[[Category: D-serine ammonia-lyase]]
	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]		[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]

OCA at 06:10, 29 June 2011

OCA — Wed, 29 Jun 2011 06:10:43 GMT

←Older revision		Revision as of 06:10, 29 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3r0z.jpg\|left\|200px]]

-	The ~~entry 3r0z~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3r0z", 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_3r0z\| PDB=3r0z \| SCENE= }}

-	~~Authors: Bharath, S.R., Shveta, B., Savithri, H.S., Murthy, M.R.N.~~	+	===Crystal structure of apo D-serine deaminase from Salmonella typhimurium===

-	~~Description~~: ~~Crystal~~ structure ~~of apo~~ D-serine ~~deaminase from~~ Salmonella typhimurium	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21668644}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21668644 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21668644}}
		+
		+	==About this Structure==
		+	[[3r0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhimurium Salmonella enterica subsp. enterica serovar typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R0Z OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021668644</ref><references group="xtra"/>
		+	[[Category: D-serine ammonia-lyase]]
		+	[[Category: Salmonella enterica subsp. enterica serovar typhimurium]]
		+	[[Category: Bharath, S R.]]
		+	[[Category: Murthy, M R.N.]]
		+	[[Category: Savithri, H S.]]
		+	[[Category: Shveta, B.]]
		+	[[Category: Alpha]]
		+	[[Category: Beta elimination of d-serine]]
		+	[[Category: Foldtype 2 family of plp-dependent enzyme]]
		+	[[Category: Lyase]]

OCA at 08:38, 6 April 2011

OCA — Wed, 06 Apr 2011 08:38:14 GMT

←Older revision		Revision as of 08:38, 6 April 2011
Line 3:		Line 3:
	The entry 3r0z is ON HOLD		The entry 3r0z is ON HOLD

-	Authors: S. R., ~~Bharath~~, ~~Bisht~~, ~~Shveta~~, H. S., ~~Savithri~~, M. R. N.~~, Murthy~~	+	Authors: Bharath, S.R., Shveta, B., Savithri, H.S., Murthy, M.R.N.

	Description: Crystal structure of apo D-serine deaminase from Salmonella typhimurium		Description: Crystal structure of apo D-serine deaminase from Salmonella typhimurium

OCA: Protected "3r0z" [edit=sysop:move=sysop]

OCA — Wed, 16 Mar 2011 08:07:37 GMT

Protected "3r0z" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:07, 16 March 2011

OCA: New page: '''Unreleased structure''' The entry 3r0z is ON HOLD Authors: S. R., Bharath, Bisht, Shveta, H. S., Savithri, M. R. N., Murthy Description: Crystal structure of apo D-serine deaminase ...

OCA — Wed, 16 Mar 2011 08:07:36 GMT

New page: '''Unreleased structure''' The entry 3r0z is ON HOLD Authors: S. R., Bharath, Bisht, Shveta, H. S., Savithri, M. R. N., Murthy Description: Crystal structure of apo D-serine deaminase ...

New page

'''Unreleased structure'''

The entry 3r0z is ON HOLD

Authors: S. R., Bharath, Bisht, Shveta, H. S., Savithri, M. R. N., Murthy

Description: Crystal structure of apo D-serine deaminase from Salmonella typhimurium