3deq - Revision history

OCA at 14:04, 13 March 2024

OCA — Wed, 13 Mar 2024 14:04:58 GMT

←Older revision		Revision as of 14:04, 13 March 2024
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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=3deq 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=3deq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.
-
-	Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.,Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Structure. 2008 Nov;16(11):1668-77. PMID:19000819<ref>PMID:19000819</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3deq" style="background-color:#fffaf0;"></div>

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

OCA at 12:46, 30 August 2023

OCA — Wed, 30 Aug 2023 12:46:01 GMT

←Older revision		Revision as of 12:46, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3deq' size='340' side='right'caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3deq' size='340' side='right'caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ALA:ALANINE'>ALA</scene>~~, ~~<scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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;~~'>~~[[3der\|3der]], [[3des\|3des]]~~</~~div~~><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">TM_0006 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])~~</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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [https://pdbe.org/3deq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [https://www.ebi.ac.uk/pdbsum/3deq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3deq 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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [https://pdbe.org/3deq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [https://www.ebi.ac.uk/pdbsum/3deq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3deq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>	+	[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thema~~]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Imker~~, H J]]~~	+	[[Category: Imker HJ]]
-	~~[[Category: Dipeptide epimerase]]~~	+
-	~~[[Category: Enzymatic function]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Thermotoga maritima~~]]	+

OCA at 07:57, 9 February 2022

OCA — Wed, 09 Feb 2022 07:57:13 GMT

←Older revision		Revision as of 07:57, 9 February 2022
Line 1:		Line 1:

	==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide==		==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide==
-	<StructureSection load='3deq' size='340' side='right' caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3deq' size='340' side='right'caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3der\|3der]], [[3des\|3des]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [~~http~~://pdbe.org/3deq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3deq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3deq 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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [https://pdbe.org/3deq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [https://www.ebi.ac.uk/pdbsum/3deq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3deq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>	+	[[https://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thema]]		[[Category: Thema]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 09:55, 14 November 2018

OCA — Wed, 14 Nov 2018 09:55:31 GMT

←Older revision		Revision as of 09:55, 14 November 2018
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=LEU:LEUCINE'>LEU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/3deq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/3deq_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 11:21, 11 August 2016

OCA — Thu, 11 Aug 2016 11:21:56 GMT

←Older revision		Revision as of 11:21, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide==		==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide==
	<StructureSection load='3deq' size='340' side='right' caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3deq' size='340' side='right' caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_maritima_msb8 Thermotoga maritima msb8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 ~~Thermotoga maritima MSB8~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [http://www.ebi.ac.uk/pdbsum/3deq 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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [http://pdbe.org/3deq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [http://www.ebi.ac.uk/pdbsum/3deq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3deq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AEEP_THEMA AEEP_THEMA]] Catalyzes the epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of a broad range of other dipeptides; is most efficient with L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His.<ref>PMID:19000819</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 16:		Line 19:
	<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=3deq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 29:
	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 3deq" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermotoga maritima msb8~~]]	+	[[Category: Thema]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Fedorov, A A]]		[[Category: Fedorov, A A]]

OCA at 08:37, 20 January 2015

OCA — Tue, 20 Jan 2015 08:37:11 GMT

←Older revision		Revision as of 08:37, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 Thermotoga maritima MSB8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 Thermotoga maritima MSB8])</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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [http://www.ebi.ac.uk/pdbsum/3deq 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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [http://www.ebi.ac.uk/pdbsum/3deq 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 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Thermotoga maritima msb8]]		[[Category: Thermotoga maritima msb8]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Fedorov, A A.]]	+	[[Category: Fedorov, A A]]
-	[[Category: Fedorov, E V.]]	+	[[Category: Fedorov, E V]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Imker, H J.]]	+	[[Category: Imker, H J]]
	[[Category: Dipeptide epimerase]]		[[Category: Dipeptide epimerase]]
	[[Category: Enzymatic function]]		[[Category: Enzymatic function]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]

OCA at 11:19, 29 September 2014

OCA — Mon, 29 Sep 2014 11:19:15 GMT

←Older revision		Revision as of 11:19, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3deq.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide==
		+	<StructureSection load='3deq' size='340' side='right' caption='[[3deq]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DEQ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3der\|3der]], [[3des\|3des]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0006 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 Thermotoga maritima MSB8])</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=3deq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3deq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3deq RCSB], [http://www.ebi.ac.uk/pdbsum/3deq 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/de/3deq_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 ==
		+	We have developed a computational approach to aid the assignment of enzymatic function for uncharacterized proteins that uses homology modeling to predict the structure of the binding site and in silico docking to identify potential substrates. We apply this method to proteins in the functionally diverse enolase superfamily that are homologous to the characterized L-Ala-D/L-Glu epimerase from Bacillus subtilis. In particular, a protein from Thermotoga martima was predicted to have different substrate specificity, which suggests that it has a different, but as yet unknown, biological function. This prediction was experimentally confirmed, resulting in the assignment of epimerase activity for L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His, whereas the enzyme is annotated incorrectly in GenBank as muconate cycloisomerase. Subsequently, crystal structures of the enzyme were determined in complex with three substrates, showing close agreement with the computational models and revealing the structural basis for the observed substrate selectivity.

-	~~{{STRUCTURE_3deq\| PDB=3deq \| SCENE= }}~~	+	Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening.,Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Structure. 2008 Nov;16(11):1668-77. PMID:19000819<ref>PMID:19000819</ref>

-	~~===Crystal structure~~ of ~~dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19000819}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3deq]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA].~~	+

	==See Also==		==See Also==
	*[[Muconate cycloisomerase\|Muconate cycloisomerase]]		*[[Muconate cycloisomerase\|Muconate cycloisomerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019000819<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermotoga maritima msb8]]		[[Category: Thermotoga maritima msb8]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA at 19:27, 20 October 2012

OCA — Sat, 20 Oct 2012 19:27:31 GMT

←Older revision		Revision as of 19:27, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3deq]] is a 4 chain structure ~~of [[Muconate cycloisomerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA].	+	[[3deq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA].

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

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

OCA — Fri, 27 Jul 2012 07:24:59 GMT

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

←Older revision

Revision as of 07:24, 27 July 2012

OCA at 07:24, 27 July 2012

OCA — Fri, 27 Jul 2012 07:24:58 GMT

←Older revision		Revision as of 07:24, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3deq.png\|left\|200px]]		[[Image:3deq.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3deq", 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.
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	{{STRUCTURE_3deq\| PDB=3deq \| SCENE= }}		{{STRUCTURE_3deq\| PDB=3deq \| SCENE= }}

	===Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide===		===Crystal structure of dipeptide epimerase from Thermotoga maritima complexed with L-Ala-L-Leu dipeptide===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19000819}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19000819 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19000819}}		{{ABSTRACT_PUBMED_19000819}}

	==About this Structure==		==About this Structure==
-	~~3DEQ~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA].	+	[[3deq]] is a 4 chain structure of [[Muconate cycloisomerase]] with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima_msb8 Thermotoga maritima msb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DEQ OCA].
		+
		+	==See Also==
		+	*[[Muconate cycloisomerase\|Muconate cycloisomerase]]

	==Reference==		==Reference==
-	Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening., Kalyanaraman C, Imker HJ, Fedorov AA, Fedorov EV, Glasner ME, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP, Structure. 2008 Nov;16(11):1668-77. PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~19000819 19000819]~~	+	<ref group="xtra">PMID:019000819</ref><references group="xtra"/>
	[[Category: Thermotoga maritima msb8]]		[[Category: Thermotoga maritima msb8]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
Line 34:		Line 25:
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Dec 5 09:54:02 2008''