6orm - Revision history

OCA at 07:15, 11 October 2023

OCA — Wed, 11 Oct 2023 07:15:44 GMT

←Older revision		Revision as of 07:15, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6orm' size='340' side='right'caption='[[6orm]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='6orm' size='340' side='right'caption='[[6orm]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6orm]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thevetia_peruviana Thevetia peruviana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ORM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6orm]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thevetia_peruviana Thevetia peruviana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ORM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.15Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=6orm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orm OCA], [~~http~~://pdbe.org/6orm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6orm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6orm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6orm 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=6orm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orm OCA], [https://pdbe.org/6orm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6orm RCSB], [https://www.ebi.ac.uk/pdbsum/6orm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6orm ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A5Q2WX04_THEPV A0A5Q2WX04_THEPV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Papain]]
	[[Category: Thevetia peruviana]]		[[Category: Thevetia peruviana]]
-	[[Category: Bezerra~~, E H.S~~]]	+	[[Category: Bezerra EHS]]
-	[[Category: Cruz~~, W T~~]]	+	[[Category: Cruz WT]]
-	[[Category: Freire~~, V N~~]]	+	[[Category: Freire VN]]
-	[[Category: Freitas~~, C D.T~~]]	+	[[Category: Freitas CDT]]
-	[[Category: Ramos~~, M V~~]]	+	[[Category: Ramos MV]]
-	[[Category: Rocha~~, B A.M~~]]	+	[[Category: Rocha BAM]]
-	[[Category: Silva~~, F M.S da]]~~	+	[[Category: Da Silva FMS]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Laticifer~~]]	+

OCA at 11:23, 26 August 2020

OCA — Wed, 26 Aug 2020 11:23:58 GMT

←Older revision		Revision as of 11:23, 26 August 2020
Line 1:		Line 1:

	==Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)==		==Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)==
-	<StructureSection load='6orm' size='340' side='right'caption='[[6orm]]' scene=''>	+	<StructureSection load='6orm' size='340' side='right'caption='[[6orm]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ORM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6orm]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thevetia_peruviana Thevetia peruviana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ORM FirstGlance]. <br>
-	</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=6orm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orm OCA], [http://pdbe.org/6orm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orm RCSB], [http://www.ebi.ac.uk/pdbsum/6orm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orm ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Papain Papain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.2 3.4.22.2] </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=6orm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orm OCA], [http://pdbe.org/6orm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orm RCSB], [http://www.ebi.ac.uk/pdbsum/6orm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orm ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peruvianin-I is a cysteine peptidase (EC 3.4.22) purified from Thevetia peruviana. Previous studies have shown that it is the only germin-like protein (GLP) with proteolytic activity described so far. In this work, the X-ray crystal structure of peruvianin-I was determined to a resolution of 2.15 A (PDB accession number: 6ORM) and its specific location was evaluated by different assays. Its overall structure shows an arrangement composed of a homohexamer (a trimer of dimers) where each monomer exhibits a typical beta-barrel fold and two glycosylation sites (Asn55 and Asn144). Analysis of its active site confirmed the absence of essential amino acids for typical oxalate oxidase activity of GLPs. Details of the active site and molecular docking results, using a specific cysteine peptidase inhibitor (iodoacetamide), were used to discuss a plausible mechanism for proteolytic activity of peruvianin-I. Histological analyses showed that T. peruviana has articulated anastomosing laticifers, i.e., rows of cells which merge to form continuous tubes throughout its green organs. Moreover, peruvianin-I was detected exclusively in the latex. Because latex peptidases have been described as defensive molecules against insects, we hypothesize that peruvianin-I contributes to protect T. peruviana plants against herbivory.
		+
		+	Crystal structure and specific location of a germin-like protein with proteolytic activity from Thevetia peruviana.,Cruz WT, Bezerra EHS, Ramos MV, Rocha BAM, Medina MC, Demarco D, Carvalho CPS, Oliveira JS, Sousa JS, Souza PFN, Freire VN, da Silva FMS, Freitas CDT Plant Sci. 2020 Sep;298:110590. doi: 10.1016/j.plantsci.2020.110590. Epub 2020, Jul 2. PMID:32771148<ref>PMID:32771148</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6orm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bezerra ~~EHS~~]]	+	[[Category: Papain]]
-	[[Category: Cruz WT]]	+	[[Category: Thevetia peruviana]]
-	[[Category: Freire VN]]	+	[[Category: Bezerra, E H.S]]
-	[[Category: Freitas ~~CDT~~]]	+	[[Category: Cruz, W T]]
-	[[Category: Ramos MV]]	+	[[Category: Freire, V N]]
-	[[Category: Rocha ~~BAM~~]]	+	[[Category: Freitas, C D.T]]
-	[[Category: Da Silva ~~FMS~~]]	+	[[Category: Ramos, M V]]
		+	[[Category: Rocha, B A.M]]
		+	[[Category: Silva, F M.S da]]
		+	[[Category: Hydrolase]]
		+	[[Category: Laticifer]]

OCA at 06:00, 6 May 2020

OCA — Wed, 06 May 2020 06:00:31 GMT

←Older revision		Revision as of 06:00, 6 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6orm ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)==
-		+	<StructureSection load='6orm' size='340' side='right'caption='[[6orm]]' scene=''>
-	~~Authors~~: ~~Cruz, W~~.T.~~, Bezerra, E~~.H.S.~~, da Silva, F~~.M.S., ~~Freire, V~~.N., ~~Ramos~~, M.V., ~~Rocha, B~~.A.M., ~~Freitas, C~~.~~D.T~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ORM FirstGlance]. <br>
-	~~Description: Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)~~	+	</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=6orm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orm OCA], [http://pdbe.org/6orm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orm RCSB], [http://www.ebi.ac.uk/pdbsum/6orm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orm ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Freire, V.N~~]]	+	__TOC__
-	[[Category: ~~Freitas, C.D.T~~]]	+	</StructureSection>
-	[[Category: ~~Bezerra, E.H.S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cruz, W.T~~]]	+	[[Category: Bezerra EHS]]
-	[[Category: ~~Da Silva, F.M.S~~]]	+	[[Category: Cruz WT]]
-	[[Category: ~~Ramos, M.V~~]]	+	[[Category: Freire VN]]
-	[[Category: ~~Rocha, B.A.M~~]]	+	[[Category: Freitas CDT]]
		+	[[Category: Ramos MV]]
		+	[[Category: Rocha BAM]]
		+	[[Category: Da Silva FMS]]

OCA at 04:28, 29 May 2019

OCA — Wed, 29 May 2019 04:28:55 GMT

←Older revision		Revision as of 04:28, 29 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6orm is ON HOLD	+	The entry 6orm is ON HOLD until Paper Publication

	Authors: Cruz, W.T., Bezerra, E.H.S., da Silva, F.M.S., Freire, V.N., Ramos, M.V., Rocha, B.A.M., Freitas, C.D.T.		Authors: Cruz, W.T., Bezerra, E.H.S., da Silva, F.M.S., Freire, V.N., Ramos, M.V., Rocha, B.A.M., Freitas, C.D.T.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Freire, V.N]]		[[Category: Freire, V.N]]
-	[[Category: Da Silva, F.M.S]]
-	[[Category: Ramos, M.V]]
	[[Category: Freitas, C.D.T]]		[[Category: Freitas, C.D.T]]
-	[[Category: Rocha, B.A.M]]
	[[Category: Bezerra, E.H.S]]		[[Category: Bezerra, E.H.S]]
	[[Category: Cruz, W.T]]		[[Category: Cruz, W.T]]
		+	[[Category: Da Silva, F.M.S]]
		+	[[Category: Ramos, M.V]]
		+	[[Category: Rocha, B.A.M]]

OCA: Protected "6orm" [edit=sysop:move=sysop]

OCA — Fri, 10 May 2019 08:03:59 GMT

Protected "6orm" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:03, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6orm is ON HOLD Authors: Cruz, W.T., Bezerra, E.H.S., da Silva, F.M.S., Freire, V.N., Ramos, M.V., Rocha, B.A.M., Freitas, C.D.T. Description: Crys...

OCA — Fri, 10 May 2019 08:03:57 GMT

New page: '''Unreleased structure''' The entry 6orm is ON HOLD Authors: Cruz, W.T., Bezerra, E.H.S., da Silva, F.M.S., Freire, V.N., Ramos, M.V., Rocha, B.A.M., Freitas, C.D.T. Description: Crys...

New page

'''Unreleased structure'''

The entry 6orm is ON HOLD

Authors: Cruz, W.T., Bezerra, E.H.S., da Silva, F.M.S., Freire, V.N., Ramos, M.V., Rocha, B.A.M., Freitas, C.D.T.

Description: Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)
[[Category: Unreleased Structures]]
[[Category: Freire, V.N]]
[[Category: Da Silva, F.M.S]]
[[Category: Ramos, M.V]]
[[Category: Freitas, C.D.T]]
[[Category: Rocha, B.A.M]]
[[Category: Bezerra, E.H.S]]
[[Category: Cruz, W.T]]