1pv9 - Revision history

OCA at 08:11, 14 February 2024

OCA — Wed, 14 Feb 2024 08:11:04 GMT

←Older revision		Revision as of 08:11, 14 February 2024
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	<StructureSection load='1pv9' size='340' side='right'caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1pv9' size='340' side='right'caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~2261 ATCC 43587])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9]~~ </~~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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [https://pdbe.org/1pv9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [https://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [~~http~~://pdbe.org/1pv9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PEPQ_PYRFU PEPQ_PYRFU]] Splits dipeptides with a prolyl in the C-terminal position and a nonpolar amino acid at the N-terminal position.<ref>PMID:9733678</ref>	+	[https://www.uniprot.org/uniprot/PEPQ_PYRFU PEPQ_PYRFU] Splits dipeptides with a prolyl in the C-terminal position and a nonpolar amino acid at the N-terminal position.<ref>PMID:9733678</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=1pv9 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=1pv9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.
-
-	Structure of the prolidase from Pyrococcus furiosus.,Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM Biochemistry. 2004 Mar 16;43(10):2771-83. PMID:15005612<ref>PMID:15005612</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pv9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Xaa-Pro dipeptidase~~]]	+	[[Category: Pyrococcus furiosus]]
-	[[Category: Adams~~, M W~~]]	+	[[Category: Adams MW]]
-	[[Category: Freeman~~, H C~~]]	+	[[Category: Freeman HC]]
-	[[Category: Ghosh, M]]	+	[[Category: Ghosh M]]
-	[[Category: Grunden~~, A M~~]]	+	[[Category: Grunden AM]]
-	[[Category: Guss~~, J M~~]]	+	[[Category: Guss JM]]
-	[[Category: Maher~~, M J~~]]	+	[[Category: Maher MJ]]
-	[[Category: Menon~~, A L]]~~	+	[[Category: Menon AL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidase]]~~	+
-	~~[[Category: Prolidase~~]]	+

OCA at 07:36, 9 December 2020

OCA — Wed, 09 Dec 2020 07:36:34 GMT

←Older revision		Revision as of 07:36, 9 December 2020
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	==Prolidase from Pyrococcus furiosus==		==Prolidase from Pyrococcus furiosus==
-	<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1pv9' size='340' side='right'caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://pdbe.org/1pv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://pdbe.org/1pv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43587]]		[[Category: Atcc 43587]]
		+	[[Category: Large Structures]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
	[[Category: Adams, M W]]		[[Category: Adams, M W]]

OCA at 08:24, 24 February 2018

OCA — Sat, 24 Feb 2018 08:24:18 GMT

←Older revision		Revision as of 08:24, 24 February 2018
Line 1:		Line 1:
		+
	==Prolidase from Pyrococcus furiosus==		==Prolidase from Pyrococcus furiosus==
	<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://pdbe.org/1pv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://pdbe.org/1pv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pv9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/1pv9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pv/1pv9_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 03:20, 9 February 2016

OCA — Tue, 09 Feb 2016 03:20:21 GMT

←Older revision		Revision as of 03:20, 9 February 2016
Line 18:		Line 18:
	<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=1pv9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:06, 10 September 2015

OCA — Thu, 10 Sep 2015 18:06:41 GMT

←Older revision		Revision as of 18:06, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus Pyrococcus furiosus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ~~Pyrococcus furiosus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://pdbe.org/1pv9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1pv9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus~~]]	+	[[Category: Atcc 43587]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
	[[Category: Adams, M W]]		[[Category: Adams, M W]]

OCA at 04:03, 25 December 2014

OCA — Thu, 25 Dec 2014 04:03:18 GMT

←Older revision		Revision as of 04:03, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 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=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PEPQ_PYRFU PEPQ_PYRFU]] Splits dipeptides with a prolyl in the C-terminal position and a nonpolar amino acid at the N-terminal position.<ref>PMID:9733678</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
-	[[Category: Adams, M W.]]	+	[[Category: Adams, M W]]
-	[[Category: Freeman, H C.]]	+	[[Category: Freeman, H C]]
-	[[Category: Ghosh, M.]]	+	[[Category: Ghosh, M]]
-	[[Category: Grunden, A M.]]	+	[[Category: Grunden, A M]]
-	[[Category: Guss, J M.]]	+	[[Category: Guss, J M]]
-	[[Category: Maher, M J.]]	+	[[Category: Maher, M J]]
-	[[Category: Menon, A L.]]	+	[[Category: Menon, A L]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Peptidase]]		[[Category: Peptidase]]
	[[Category: Prolidase]]		[[Category: Prolidase]]

OCA at 21:18, 28 September 2014

OCA — Sun, 28 Sep 2014 21:18:07 GMT

←Older revision		Revision as of 21:18, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1pv9.~~png~~\|~~left~~\|200px]]	+	==Prolidase from Pyrococcus furiosus==
		+	<StructureSection load='1pv9' size='340' side='right' caption='[[1pv9]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PV9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PEPQ OR PF1343 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xaa-Pro_dipeptidase Xaa-Pro dipeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.13.9 3.4.13.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pv9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pv9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pv9 RCSB], [http://www.ebi.ac.uk/pdbsum/1pv9 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/pv/1pv9_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 structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.

-	~~{{STRUCTURE_1pv9\| PDB=1pv9 \| SCENE= }}~~	+	Structure of the prolidase from Pyrococcus furiosus.,Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM Biochemistry. 2004 Mar 16;43(10):2771-83. PMID:15005612<ref>PMID:15005612</ref>

-	~~===Prolidase from Pyrococcus furiosus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15005612}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1pv9]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015005612<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]

OCA: Protected "1pv9" [edit=sysop:move=sysop]

OCA — Wed, 19 Dec 2012 12:00:36 GMT

Protected "1pv9" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:00, 19 December 2012

OCA at 12:00, 19 December 2012

OCA — Wed, 19 Dec 2012 12:00:34 GMT

←Older revision		Revision as of 12:00, 19 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pv9.png\|left\|200px]]		[[Image:1pv9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pv9", 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_1pv9\| PDB=1pv9 \| SCENE= }}		{{STRUCTURE_1pv9\| PDB=1pv9 \| SCENE= }}

	===Prolidase from Pyrococcus furiosus===		===Prolidase from Pyrococcus furiosus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15005612}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15005612 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15005612}}		{{ABSTRACT_PUBMED_15005612}}

	==About this Structure==		==About this Structure==
-	~~1PV9~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].	+	[[1pv9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15005612~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015005612</ref><references group="xtra"/>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
Line 33:		Line 21:
	[[Category: Maher, M J.]]		[[Category: Maher, M J.]]
	[[Category: Menon, A L.]]		[[Category: Menon, A L.]]
		+	[[Category: Hydrolase]]
	[[Category: Peptidase]]		[[Category: Peptidase]]
	[[Category: Prolidase]]		[[Category: Prolidase]]
-	[[Category: Zinc]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:03:25 2009''

OCA at 04:03, 17 February 2009

OCA — Tue, 17 Feb 2009 04:03:26 GMT

←Older revision		Revision as of 04:03, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PV9 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].	+	1PV9 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PV9 OCA].

	==Reference==		==Reference==
-	~~Structure of the prolidase from Pyrococcus furiosus., Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM, Biochemistry. 2004 Mar 16;43(10):2771-83.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15005612 15005612]~~	+	<ref group="xtra">PMID:15005612</ref><references group="xtra"/>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
-	[[Category: Single protein]]
	[[Category: Xaa-Pro dipeptidase]]		[[Category: Xaa-Pro dipeptidase]]
	[[Category: Adams, M W.]]		[[Category: Adams, M W.]]
Line 38:		Line 37:
	[[Category: Zinc]]		[[Category: Zinc]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 09~~:31:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:03:25 2009''