5z48 - Revision history

OCA at 08:44, 22 November 2023

OCA — Wed, 22 Nov 2023 08:44:58 GMT

←Older revision		Revision as of 08:44, 22 November 2023
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	<StructureSection load='5z48' size='340' side='right'caption='[[5z48]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='5z48' size='340' side='right'caption='[[5z48]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z48]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Deira Deira~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z48 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Z48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z48]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z48 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z48 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene~~>, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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]] 1.551Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~pcp, DR_0490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=243230 DEIRA])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Pyroglutamyl-peptidase_I Pyroglutamyl-peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.3 3.4.19.3]~~ </~~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=5z48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z48 OCA], [https://pdbe.org/5z48 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z48 RCSB], [https://www.ebi.ac.uk/pdbsum/5z48 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z48 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=5z48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z48 OCA], [~~http~~://pdbe.org/5z48 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5z48 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5z48 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5z48 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCP_DEIRA PCP_DEIRA]] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.	+	[https://www.uniprot.org/uniprot/PCP_DEIRA PCP_DEIRA] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira~~]]	+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Pyroglutamyl-peptidase I]]~~	+	[[Category: Agrawal R]]
-	[[Category: Agrawal, R]]	+	[[Category: Kumar A]]
-	[[Category: Kumar, A]]	+	[[Category: Makde RD]]
-	[[Category: Makde~~, R D]]~~	+
-	~~[[Category: Exopeptidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Omega peptidase]]~~	+
-	~~[[Category: Pyroglutamate~~]]	+

OCA at 06:33, 17 April 2019

OCA — Wed, 17 Apr 2019 06:33:13 GMT

←Older revision		Revision as of 06:33, 17 April 2019
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	==Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate==		==Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate==
-	<StructureSection load='5z48' size='340' side='right' caption='[[5z48]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='5z48' size='340' side='right'caption='[[5z48]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5z48]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z48 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5z48]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z48 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pcp, DR_0490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyroglutamyl-peptidase_I Pyroglutamyl-peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.3 3.4.19.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyroglutamyl-peptidase_I Pyroglutamyl-peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.3 3.4.19.3] </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=5z48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z48 OCA], [http://pdbe.org/5z48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z48 RCSB], [http://www.ebi.ac.uk/pdbsum/5z48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z48 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=5z48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z48 OCA], [http://pdbe.org/5z48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z48 RCSB], [http://www.ebi.ac.uk/pdbsum/5z48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z48 ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PCP_DEIRA PCP_DEIRA]] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.		[[http://www.uniprot.org/uniprot/PCP_DEIRA PCP_DEIRA]] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyrrolidone-carboxylate peptidase (PCP) catalyzes the removal of an unusual amino acid, L-pyroglutamate (pG), from the N-termini of peptides and proteins. It has implications in the functional regulation of different peptides in both prokaryotes and eukaryotes. However, the pG-recognition mechanism of the PCP enzyme remains largely unknown. Here, crystal structures of PCP I from Deinococcus radiodurans (PCPdr) are reported in pG-free and pG-bound forms at resolutions of 1.73 and 1.55 A, respectively. Four protomers in PCPdr form a tetrameric structure. The residues responsible for recognizing the pG residue are mostly contributed by a flexible loop (loop A) that is present near the active site. These residues are conserved in all known PCPs I, including those from mammals. Phe9 and Phe12 of loop A form stacking interactions with the pyrrolidone ring of pG, while Asn18 forms a hydrogen bond to OE of pG. The main chain of a nonconserved residue, Leu71, forms two hydrogen bonds to NH and OE of pG. Thus, pG is recognized in the S1 substrate subsite of the enzyme by both van der Waals and polar interactions, which provide specificity for the pG residue of the peptide. In contrast to previously reported PCP I structures, the PCPdr tetramer is in a closed conformation with an inaccessible active site. The structures show that the active site can be accessed by the substrates via disordering of loop A. This disordering could also prevent product inhibition by releasing the bound pG product from the S1 subsite, thus allowing the enzyme to engage a fresh substrate.
		+
		+	Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition.,Agrawal R, Singh R, Kumar A, Kumar A, Makde RD Acta Crystallogr D Struct Biol. 2019 Mar 1;75(Pt 3):308-316. doi:, 10.1107/S2059798319000676. Epub 2019 Feb 28. PMID:30950401<ref>PMID:30950401</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5z48" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
		+	[[Category: Large Structures]]
	[[Category: Pyroglutamyl-peptidase I]]		[[Category: Pyroglutamyl-peptidase I]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]

OCA at 11:57, 16 January 2019

OCA — Wed, 16 Jan 2019 11:57:53 GMT

←Older revision		Revision as of 11:57, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5z48 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate==
-		+	<StructureSection load='5z48' size='340' side='right' caption='[[5z48]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~Authors~~: ~~Agrawal~~, R., ~~Kumar~~, A., ~~Kumar~~, A., ~~Makde, R~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5z48]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z48 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z48 FirstGlance]. <br>
-	~~Description: Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyroglutamyl-peptidase_I Pyroglutamyl-peptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.3 3.4.19.3] </span></td></tr>
-	[[Category: ~~Makde, R.D~~]]	+	<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=5z48 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z48 OCA], [http://pdbe.org/5z48 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z48 RCSB], [http://www.ebi.ac.uk/pdbsum/5z48 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z48 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCP_DEIRA PCP_DEIRA]] Removes 5-oxoproline from various penultimate amino acid residues except L-proline.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pyroglutamyl-peptidase I]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Exopeptidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Omega peptidase]]
		+	[[Category: Pyroglutamate]]

OCA at 05:01, 12 December 2018

OCA — Wed, 12 Dec 2018 05:01:52 GMT

←Older revision		Revision as of 05:01, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z48 is ON HOLD	+	The entry 5z48 is ON HOLD until Paper Publication

	Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D.		Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D.

OCA at 18:24, 2 December 2018

OCA — Sun, 02 Dec 2018 18:24:22 GMT

←Older revision		Revision as of 18:24, 2 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z48 is ON HOLD ~~until Paper Publication~~	+	The entry 5z48 is ON HOLD

-	Authors: Agrawal, R., Kumar, A., ~~Ghosh~~, B., Makde, R.D.	+	Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D.

-	Description: Crystal structure of pyrrolidone carboxylate peptidase I from ~~Deionococcus~~ radiodurans R1 bound to pyroglutamate	+	Description: Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Makde, R.D]]		[[Category: Makde, R.D]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
-	[[Category: Ghosh, B]]

OCA at 04:58, 7 February 2018

OCA — Wed, 07 Feb 2018 04:58:19 GMT

←Older revision		Revision as of 04:58, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5z48 is ON HOLD	+	The entry 5z48 is ON HOLD until Paper Publication

	Authors: Agrawal, R., Kumar, A., Ghosh, B., Makde, R.D.		Authors: Agrawal, R., Kumar, A., Ghosh, B., Makde, R.D.

OCA at 17:11, 24 January 2018

OCA — Wed, 24 Jan 2018 17:11:01 GMT

←Older revision		Revision as of 17:11, 24 January 2018
Line 3:		Line 3:
	The entry 5z48 is ON HOLD		The entry 5z48 is ON HOLD

-	Authors: Agrawal, R., Kumar, A., Ghosh, B~~., Kumar, A~~., Makde, R.D.	+	Authors: Agrawal, R., Kumar, A., Ghosh, B., Makde, R.D.

	Description: Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1 bound to pyroglutamate		Description: Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1 bound to pyroglutamate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Agrawal, R]]
	[[Category: Makde, R.D]]		[[Category: Makde, R.D]]
		+	[[Category: Agrawal, R]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
	[[Category: Ghosh, B]]		[[Category: Ghosh, B]]

OCA: Protected "5z48" [edit=sysop:move=sysop]

OCA — Wed, 17 Jan 2018 05:34:18 GMT

Protected "5z48" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:34, 17 January 2018

OCA: New page: '''Unreleased structure''' The entry 5z48 is ON HOLD Authors: Agrawal, R., Kumar, A., Ghosh, B., Kumar, A., Makde, R.D. Description: Crystal structure of pyrrolidone carboxylate peptid...

OCA — Wed, 17 Jan 2018 05:34:16 GMT

New page: '''Unreleased structure''' The entry 5z48 is ON HOLD Authors: Agrawal, R., Kumar, A., Ghosh, B., Kumar, A., Makde, R.D. Description: Crystal structure of pyrrolidone carboxylate peptid...

New page

'''Unreleased structure'''

The entry 5z48 is ON HOLD

Authors: Agrawal, R., Kumar, A., Ghosh, B., Kumar, A., Makde, R.D.

Description: Crystal structure of pyrrolidone carboxylate peptidase I from Deionococcus radiodurans R1 bound to pyroglutamate
[[Category: Unreleased Structures]]
[[Category: Agrawal, R]]
[[Category: Makde, R.D]]
[[Category: Kumar, A]]
[[Category: Ghosh, B]]