5yzm - Revision history

OCA at 08:42, 22 November 2023

OCA — Wed, 22 Nov 2023 08:42:08 GMT

←Older revision		Revision as of 08:42, 22 November 2023
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	<StructureSection load='5yzm' size='340' side='right'caption='[[5yzm]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5yzm' size='340' side='right'caption='[[5yzm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzm]] is a 4 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=5YZM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YZM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzm]] is a 4 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=5YZM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YZM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</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">~~DR_0165 ([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=ACT:ACETATE+ION'>ACT</scene></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=5yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzm OCA], [~~http~~://pdbe.org/5yzm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yzm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yzm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzm 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=5yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzm OCA], [https://pdbe.org/5yzm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yzm RCSB], [https://www.ebi.ac.uk/pdbsum/5yzm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RXY9_DEIRA Q9RXY9_DEIRA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Deira~~]]	+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ghosh, B]]	+	[[Category: Ghosh B]]
-	[[Category: Jamdar~~, S N~~]]	+	[[Category: Jamdar SN]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	[[Category: Makde~~, R D~~]]	+	[[Category: Makde RD]]
-	[[Category: Yadav, P]]	+	[[Category: Yadav P]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Merops s9]]~~	+
-	~~[[Category: Pop family]]~~	+
-	~~[[Category: Serine peptidase~~]]	+

OCA at 17:06, 20 November 2019

OCA — Wed, 20 Nov 2019 17:06:13 GMT

←Older revision		Revision as of 17:06, 20 November 2019
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	==Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1==		==Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1==
-	<StructureSection load='5yzm' size='340' side='right' caption='[[5yzm]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5yzm' size='340' side='right'caption='[[5yzm]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yzm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yzm]] is a 4 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=5YZM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_0165 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=5yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzm OCA], [http://pdbe.org/5yzm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzm RCSB], [http://www.ebi.ac.uk/pdbsum/5yzm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzm 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=5yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzm OCA], [http://pdbe.org/5yzm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzm RCSB], [http://www.ebi.ac.uk/pdbsum/5yzm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Serine peptidases of the prolyl oligopeptidase (POP) family are of substantial therapeutic importance because of their involvement in diseases such as diabetes, cancer, neurological diseases, and autoimmune disorders. Proper annotation and knowledge of substrate specificity mechanisms in this family are highly valuable. Although endopeptidase, dipeptidyl peptidase, tripeptidyl peptidase, and acylaminoacyl peptidase activities have been reported previously, here we report the first instance of carboxypeptidase activity in a POP family member. We determined the crystal structures of this carboxypeptidase, an S9C subfamily member from Deinococcus radiodurans, in its active and inactive states at 2.3-A resolution, providing an unprecedented view of assembly and disassembly of the active site mediated by an arginine residue. We observed that this residue is poised to bind substrate in the active structure and disrupts the catalytic triad in the inactive structure. The assembly of the active site is accompanied by the ordering of gating loops, which reduces the effective size of the oligomeric pore. This prevents the entry of larger peptides and constitutes a novel mechanism for substrate screening. Furthermore, we observed structural adaptations that enable its carboxypeptidase activity, with a unique loop and two arginine residues in the active site cavity orienting the peptide substrate for catalysis. Using these structural features, we identified homologs of this enzyme in the POP family and confirmed the presence of carboxypeptidase activity in one of them. In conclusion, we have identified a new type within POP enzymes that exhibits not only unique activity but also a novel substrate-screening mechanism.
		+
		+	Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.,Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Jamdar SN, Makde RD J Biol Chem. 2019 Jan 4;294(1):89-100. doi: 10.1074/jbc.RA118.004254. Epub 2018, Nov 8. PMID:30409909<ref>PMID:30409909</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yzm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
		+	[[Category: Large Structures]]
	[[Category: Ghosh, B]]		[[Category: Ghosh, B]]
	[[Category: Jamdar, S N]]		[[Category: Jamdar, S N]]

OCA at 08:04, 14 November 2018

OCA — Wed, 14 Nov 2018 08:04:49 GMT

←Older revision		Revision as of 08:04, 14 November 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5yzm is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1==
-		+	<StructureSection load='5yzm' size='340' side='right' caption='[[5yzm]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Yadav, P~~., ~~Jamdar, S~~.N., ~~Kumar~~, A., ~~Ghosh, B~~., ~~Makde, R~~.D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yzm]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YZM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YZM FirstGlance]. <br>
-	~~Description: Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
-	~~[[Category: Unreleased Structures]]~~	+	<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=5yzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yzm OCA], [http://pdbe.org/5yzm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yzm RCSB], [http://www.ebi.ac.uk/pdbsum/5yzm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yzm ProSAT]</span></td></tr>
-	[[Category: ~~Makde~~, ~~R.D~~]]	+	</table>
-	[[Category: Jamdar, S.N]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Ghosh, B]]
		+	[[Category: Jamdar, S N]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
-	[[Category: ~~Ghosh~~, B]]	+	[[Category: Makde, R D]]
	[[Category: Yadav, P]]		[[Category: Yadav, P]]
		+	[[Category: Hydrolase]]
		+	[[Category: Merops s9]]
		+	[[Category: Pop family]]
		+	[[Category: Serine peptidase]]

OCA at 03:48, 20 June 2018

OCA — Wed, 20 Jun 2018 03:48:42 GMT

←Older revision		Revision as of 03:48, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.		Authors: Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.

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

OCA — Wed, 20 Dec 2017 04:54:02 GMT

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

←Older revision

Revision as of 04:54, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yzm is ON HOLD Authors: Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D. Description: Crystal structure of S9 peptidase (inactive form) ...

OCA — Wed, 20 Dec 2017 04:54:00 GMT

New page: '''Unreleased structure''' The entry 5yzm is ON HOLD Authors: Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D. Description: Crystal structure of S9 peptidase (inactive form) ...

New page

'''Unreleased structure'''

The entry 5yzm is ON HOLD

Authors: Yadav, P., Jamdar, S.N., Kumar, A., Ghosh, B., Makde, R.D.

Description: Crystal structure of S9 peptidase (inactive form) from Deinococcus radiodurans R1
[[Category: Unreleased Structures]]
[[Category: Makde, R.D]]
[[Category: Jamdar, S.N]]
[[Category: Kumar, A]]
[[Category: Ghosh, B]]
[[Category: Yadav, P]]