3ro6 - Revision history

OCA at 09:44, 1 March 2024

OCA — Fri, 01 Mar 2024 09:44:11 GMT

←Older revision		Revision as of 09:44, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3ro6' size='340' side='right'caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3ro6' size='340' side='right'caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Acm_1292 Acm 1292~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RO6 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=MG:MAGNESIUM+ION'>MG</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3rit\|3rit]]~~</~~div~~><~~/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=MG:MAGNESIUM+ION'>MG</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">MCA1834 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 ACM 1292])~~</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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [https://pdbe.org/3ro6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ro6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ro6 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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [https://pdbe.org/3ro6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ro6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ro6 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/KRDE_METCA KRDE_METCA] Catalyzes the epimerization of L-Lys-L-Arg to L-Lys-D-Arg. Can also catalyze the epimerization of other cationic dipeptides, such as L-Arg-L-Arg, L-Lys-L-Lys and L-Lys-L-His, but with lower efficiency (in vitro).<ref>PMID:22392983</ref>
-	The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. ~~Here we describe~~ the ~~results~~ of ~~a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala~~-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-~~Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala~~-~~Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D~~-~~Ala~~-D-~~Ala; and (iii) a small group~~ of ~~enzymes that epimerize~~ cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, ~~large~~-~~scale fashion.~~	+
-		+
-	~~Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.~~,~~Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song~~ L, ~~Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109~~(11)~~:4122-7~~. ~~Epub 2012 Mar 5. PMID:22392983~~<ref>PMID:22392983</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ro6" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Acm 1292]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Methylococcus capsulatus]]
-	[[Category: Lukk, T]]	+	[[Category: Gerlt JA]]
-	[[Category: Nair~~, S K~~]]	+	[[Category: Lukk T]]
-	[[Category: Sakai, A]]	+	[[Category: Nair SK]]
-	[[Category: Song, L]]	+	[[Category: Sakai A]]
-	~~[[Category: Isomerase]]~~	+	[[Category: Song L]]
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:19, 22 June 2022

OCA — Wed, 22 Jun 2022 10:19:15 GMT

←Older revision		Revision as of 10:19, 22 June 2022
Line 1:		Line 1:

	==Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion==		==Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion==
-	<StructureSection load='3ro6' size='340' side='right' caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='3ro6' size='340' side='right'caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Acm_1292 Acm 1292]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acm_1292 Acm 1292]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RO6 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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">[[3rit\|3rit]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3rit\|3rit]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 ACM 1292])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 ACM 1292])</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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [~~http~~://pdbe.org/3ro6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ro6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ro6 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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [https://pdbe.org/3ro6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ro6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ro6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Acm 1292]]		[[Category: Acm 1292]]
		+	[[Category: Large Structures]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Lukk, T]]		[[Category: Lukk, T]]

OCA at 09:57, 11 August 2016

OCA — Thu, 11 Aug 2016 09:57:29 GMT

←Older revision		Revision as of 09:57, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion==		==Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion==
	<StructureSection load='3ro6' size='340' side='right' caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='3ro6' size='340' side='right' caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methylococcus_capsulatus Methylococcus capsulatus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RO6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Acm_1292 Acm 1292]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RO6 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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">[[3rit\|3rit]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rit\|3rit]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 ~~Methylococcus capsulatus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 ACM 1292])</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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ro6 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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [http://pdbe.org/3ro6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ro6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ro6 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3ro6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methylococcus capsulatus~~]]	+	[[Category: Acm 1292]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
	[[Category: Lukk, T]]		[[Category: Lukk, T]]

OCA at 10:23, 4 January 2015

OCA — Sun, 04 Jan 2015 10:23:02 GMT

←Older revision		Revision as of 10:23, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RO6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RO6 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=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rit\|3rit]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rit\|3rit]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 Methylococcus capsulatus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 Methylococcus capsulatus])</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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ro6 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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ro6 PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 14:
	Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983<ref>PMID:22392983</ref>		Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983<ref>PMID:22392983</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Lukk, T.]]	+	[[Category: Lukk, T]]
-	[[Category: Nair, S K.]]	+	[[Category: Nair, S K]]
-	[[Category: Sakai, A.]]	+	[[Category: Sakai, A]]
-	[[Category: Song, L.]]	+	[[Category: Song, L]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 04:45, 5 June 2014

OCA — Thu, 05 Jun 2014 04:45:47 GMT

←Older revision		Revision as of 04:45, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3ro6.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion==
		+	<StructureSection load='3ro6' size='340' side='right' caption='[[3ro6]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RO6 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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3rit\|3rit]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MCA1834 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=414 Methylococcus capsulatus])</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=3ro6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ro6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ro6 RCSB], [http://www.ebi.ac.uk/pdbsum/3ro6 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion.

-	~~<!--~~	+	Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.,Lukk T, Sakai A, Kalyanaraman C, Brown SD, Imker HJ, Song L, Fedorov AA, Fedorov EV, Toro R, Hillerich B, Seidel R, Patskovsky Y, Vetting MW, Nair SK, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4122-7. Epub 2012 Mar 5. PMID:22392983<ref>PMID:22392983</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3ro6"~~, ~~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_3ro6\| PDB=3ro6 \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22392983}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22392983 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22392983}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ro6]] is a 6 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022392983<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]

OCA at 06:25, 21 March 2012

OCA — Wed, 21 Mar 2012 06:25:36 GMT

←Older revision		Revision as of 06:25, 21 March 2012
Line 11:		Line 11:
	===Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion===		===Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22392983}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22392983 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22392983}}

	==About this Structure==		==About this Structure==
	[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA].		[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022392983</ref><references group="xtra"/>
	[[Category: Methylococcus capsulatus]]		[[Category: Methylococcus capsulatus]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]

OCA at 06:47, 22 February 2012

OCA — Wed, 22 Feb 2012 06:47:16 GMT

←Older revision		Revision as of 06:47, 22 February 2012
Line 20:		Line 20:
	[[Category: Sakai, A.]]		[[Category: Sakai, A.]]
	[[Category: Song, L.]]		[[Category: Song, L.]]
		+	[[Category: Isomerase]]
		+	[[Category: Tim barrel]]

OCA at 06:03, 18 May 2011

OCA — Wed, 18 May 2011 06:03:08 GMT

←Older revision		Revision as of 06:03, 18 May 2011
Line 1:		Line 1:
-	[[Image:3ro6.~~jpg~~\|left\|200px]]	+	[[Image:3ro6.png\|left\|200px]]

	<!--		<!--

OCA at 04:56, 12 May 2011

OCA — Thu, 12 May 2011 04:56:45 GMT

←Older revision		Revision as of 04:56, 12 May 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ro6.jpg\|left\|200px]]

-	The ~~entry 3ro6~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ro6", 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_3ro6\| PDB=3ro6 \| SCENE= }}

-	~~Authors: Lukk, T., Sakai, A., Song, L., Gerlt, J.A., Nair, S.K.~~	+	===Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg ion===

-	~~Description: Crystal~~ structure ~~of Dipeptide Epimerase~~ from Methylococcus capsulatus ~~complexed with Mg ion~~	+
		+	==About this Structure==
		+	[[3ro6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Methylococcus_capsulatus Methylococcus capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RO6 OCA].
		+	[[Category: Methylococcus capsulatus]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Lukk, T.]]
		+	[[Category: Nair, S K.]]
		+	[[Category: Sakai, A.]]
		+	[[Category: Song, L.]]

OCA: Protected "3ro6" [edit=sysop:move=sysop]

OCA — Wed, 04 May 2011 06:34:12 GMT

Protected "3ro6" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:34, 4 May 2011