3lom - Revision history

OCA at 10:21, 21 February 2024

OCA — Wed, 21 Feb 2024 10:21:32 GMT

←Older revision		Revision as of 10:21, 21 February 2024
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila==		==CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila==
-	<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3lom' size='340' side='right'caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lom]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Legph Legph~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lom]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._Philadelphia_1 Legionella pneumophila subsp. pneumophila str. Philadelphia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LOM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.3Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ispA, lpg2330 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=272624 LEGPH])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10]~~ </~~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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [https://pdbe.org/3lom PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [https://www.ebi.ac.uk/pdbsum/3lom PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lom ProSAT]</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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [~~http~~://pdbe.org/3lom PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lom PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lom ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5ZT35_LEGPH Q5ZT35_LEGPH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=3lom 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=3lom ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value </= 1e-70) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.
-
-	Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.,Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD Proc Natl Acad Sci U S A. 2013 Mar 14. PMID:23493556<ref>PMID:23493556</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3lom" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Legph~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Almo, S C~~]]	+	[[Category: Legionella pneumophila subsp. pneumophila str. Philadelphia 1]]
-	[[Category: ~~Burley, S K~~]]	+	[[Category: Almo SC]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Burley SK]]
-	[[Category: Patskovsky, Y]]	+	[[Category: Patskovsky Y]]
-	[[Category: Rutter, M]]	+	[[Category: Rutter M]]
-	[[Category: Sauder~~, J M~~]]	+	[[Category: Sauder JM]]
-	[[Category: Toro, R]]	+	[[Category: Toro R]]
-	~~[[Category: Geranyltransferase]]~~	+
-	~~[[Category: Isoprene biosynthesis]]~~	+
-	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:19, 9 January 2019

OCA — Wed, 09 Jan 2019 07:19:32 GMT

←Older revision		Revision as of 07:19, 9 January 2019
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila==		==CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila==
	<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispA, lpg2330 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 LEGPH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispA, lpg2330 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 LEGPH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [http://pdbe.org/3lom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [http://www.ebi.ac.uk/pdbsum/3lom 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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [http://pdbe.org/3lom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [http://www.ebi.ac.uk/pdbsum/3lom PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lom ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lo/3lom_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lo/3lom_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 00:51, 8 February 2016

OCA — Mon, 08 Feb 2016 00:51:09 GMT

←Older revision		Revision as of 00:51, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lom]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Legionella_pneumophila_subsp._pneumophila_str._philadelphia_1 Legionella pneumophila subsp. pneumophila str. philadelphia 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LOM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lom]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Legph Legph]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LOM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispA, lpg2330 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 ~~Legionella pneumophila subsp. pneumophila str. Philadelphia 1~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispA, lpg2330 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 LEGPH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [http://www.ebi.ac.uk/pdbsum/3lom 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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [http://pdbe.org/3lom PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [http://www.ebi.ac.uk/pdbsum/3lom PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=3lom ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 3lom" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Legionella pneumophila subsp. pneumophila str. philadelphia 1~~]]	+	[[Category: Legph]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 13:31, 6 November 2014

OCA — Thu, 06 Nov 2014 13:31:55 GMT

←Older revision		Revision as of 13:31, 6 November 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3lom~~\| ~~PDB~~=3lom \| ~~SCENE~~= }}	+	==CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila==
-	===~~CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM~~ Legionella pneumophila===	+	<StructureSection load='3lom' size='340' side='right' caption='[[3lom]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23493556}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lom]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._philadelphia_1 Legionella pneumophila subsp. pneumophila str. philadelphia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LOM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispA, lpg2330 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272624 Legionella pneumophila subsp. pneumophila str. Philadelphia 1])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(2E,6E)-farnesyl_diphosphate_synthase (2E,6E)-farnesyl diphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.10 2.5.1.10] </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=3lom FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lom OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lom RCSB], [http://www.ebi.ac.uk/pdbsum/3lom 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/lo/3lom_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 ==
		+	The number of available protein sequences has increased exponentially with the advent of high-throughput genomic sequencing, creating a significant challenge for functional annotation. Here, we describe a large-scale study on assigning function to unknown members of the trans-polyprenyl transferase (E-PTS) subgroup in the isoprenoid synthase superfamily, which provides substrates for the biosynthesis of the more than 55,000 isoprenoid metabolites. Although the mechanism for determining the product chain length for these enzymes is known, there is no simple relationship between function and primary sequence, so that assigning function is challenging. We addressed this challenge through large-scale bioinformatics analysis of >5,000 putative polyprenyl transferases; experimental characterization of the chain-length specificity of 79 diverse members of this group; determination of 27 structures of 19 of these enzymes, including seven cocrystallized with substrate analogs or products; and the development and successful application of a computational approach to predict function that leverages available structural data through homology modeling and docking of possible products into the active site. The crystallographic structures and computational structural models of the enzyme-ligand complexes elucidate the structural basis of specificity. As a result of this study, the percentage of E-PTS sequences similar to functionally annotated ones (BLAST e-value </= 1e-70) increased from 40.6 to 68.8%, and the percentage of sequences similar to available crystal structures increased from 28.9 to 47.4%. The high accuracy of our blind prediction of newly characterized enzymes indicates the potential to predict function to the complete polyprenyl transferase subgroup of the isoprenoid synthase superfamily computationally.

-	~~==About this Structure==~~	+	Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.,Wallrapp FH, Pan JJ, Ramamoorthy G, Almonacid DE, Hillerich BS, Seidel R, Patskovsky Y, Babbitt PC, Almo SC, Jacobson MP, Poulter CD Proc Natl Acad Sci U S A. 2013 Mar 14. PMID:23493556<ref>PMID:23493556</ref>
-	~~[[3lom]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._philadelphia_1 Legionella pneumophila subsp~~. ~~pneumophila str~~. ~~philadelphia 1]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin~~/~~ocashort?id=3LOM OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Legionella pneumophila subsp. pneumophila str. philadelphia 1]]		[[Category: Legionella pneumophila subsp. pneumophila str. philadelphia 1]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Burley, S K.]]	+	[[Category: Burley, S K]]
-	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Patskovsky, Y.]]	+	[[Category: Patskovsky, Y]]
-	[[Category: Rutter, M.]]	+	[[Category: Rutter, M]]
-	[[Category: Sauder, J M.]]	+	[[Category: Sauder, J M]]
-	[[Category: Toro, R.]]	+	[[Category: Toro, R]]
	[[Category: Geranyltransferase]]		[[Category: Geranyltransferase]]
	[[Category: Isoprene biosynthesis]]		[[Category: Isoprene biosynthesis]]
-	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~	+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-	~~[[Category: New york structural genomix research consortium~~]]	+
	[[Category: Nysgrc]]		[[Category: Nysgrc]]
-	[[Category: ~~Nysgxrc]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+
	[[Category: Transferase]]		[[Category: Transferase]]

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

OCA — Wed, 27 Mar 2013 07:54:36 GMT

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

←Older revision

Revision as of 07:54, 27 March 2013

OCA at 07:54, 27 March 2013

OCA — Wed, 27 Mar 2013 07:54:34 GMT

←Older revision		Revision as of 07:54, 27 March 2013
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-	{{Seed}}
-	[[Image:3lom.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lom", 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_3lom\| PDB=3lom \| SCENE= }}		{{STRUCTURE_3lom\| PDB=3lom \| SCENE= }}
-
	===CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila===		===CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila===
-		+	{{ABSTRACT_PUBMED_23493556}}

	==About this Structure==		==About this Structure==
-	~~3LOM~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp.~~_pneumophila~~ Legionella pneumophila subsp. pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA].	+	[[3lom]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila_str._philadelphia_1 Legionella pneumophila subsp. pneumophila str. philadelphia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA].
-	~~[[Category: Geranyltranstransferase]]~~	+	[[Category: Legionella pneumophila subsp. pneumophila str. philadelphia 1]]
-	[[Category: Legionella pneumophila subsp. pneumophila]]	+
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]
Line 34:		Line 23:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 10:57:07 2010''

OCA at 08:57, 17 February 2010

OCA — Wed, 17 Feb 2010 08:57:08 GMT

←Older revision		Revision as of 08:57, 17 February 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3lom.jpg\|left\|200px]]

-	The ~~entry 3lom~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lom", 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_3lom\| PDB=3lom \| SCENE= }}

-	~~Authors: Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C.~~	+	===CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila===

-	Description: CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:00:36 2010''	+	==About this Structure==
		+	3LOM is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Legionella_pneumophila_subsp._pneumophila Legionella pneumophila subsp. pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LOM OCA].
		+	[[Category: Geranyltranstransferase]]
		+	[[Category: Legionella pneumophila subsp. pneumophila]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Burley, S K.]]
		+	[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
		+	[[Category: Patskovsky, Y.]]
		+	[[Category: Rutter, M.]]
		+	[[Category: Sauder, J M.]]
		+	[[Category: Toro, R.]]
		+	[[Category: Geranyltransferase]]
		+	[[Category: Isoprene biosynthesis]]
		+	[[Category: New york sgx research center for structural genomic]]
		+	[[Category: New york structural genomix research consortium]]
		+	[[Category: Nysgrc]]
		+	[[Category: Nysgxrc]]
		+	[[Category: Protein structure initiative]]
		+	[[Category: Psi]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 17 10:57:07 2010''

OCA: New page: '''Unreleased structure''' The entry 3lom is ON HOLD Authors: Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C. Description: CRYSTAL STRUCTURE OF GERANYLTRAN...

OCA — Wed, 10 Feb 2010 15:00:36 GMT

New page: '''Unreleased structure''' The entry 3lom is ON HOLD Authors: Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C. Description: CRYSTAL STRUCTURE OF GERANYLTRAN...

New page

'''Unreleased structure'''

The entry 3lom is ON HOLD

Authors: Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C.

Description: CRYSTAL STRUCTURE OF GERANYLTRANSFERASE FROM Legionella pneumophila

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 10 17:00:36 2010''