6iru - Revision history

OCA at 09:52, 22 November 2023

2023-11-22T09:52:03Z

←Older revision		Revision as of 09:52, 22 November 2023
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	<StructureSection load='6iru' size='340' side='right'caption='[[6iru]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='6iru' size='340' side='right'caption='[[6iru]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iru]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IRU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IRU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iru]] is a 3 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=6IRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IRU FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">[[~~6a4t~~\|~~6a4t~~]]</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]] 2.7Å</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=6iru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iru OCA], [~~http~~://pdbe.org/6iru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iru 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=6iru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iru OCA], [https://pdbe.org/6iru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iru RCSB], [https://www.ebi.ac.uk/pdbsum/6iru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iru ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Y1070_DEIRA Y1070_DEIRA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chandravanshi, K]]	+	[[Category: Chandravanshi K]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	[[Category: Makde~~, R D~~]]	+	[[Category: Makde RD]]
-	[[Category: Yadav, P]]	+	[[Category: Yadav P]]
-	~~[[Category: Active site]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Esterase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Peptidase e]]~~	+
-	~~[[Category: S51 peptidase~~]]	+

OCA at 15:21, 20 November 2019

2019-11-20T15:21:01Z

←Older revision		Revision as of 15:21, 20 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6iru is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group==
		+	<StructureSection load='6iru' size='340' side='right'caption='[[6iru]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6iru]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IRU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IRU FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6a4t\|6a4t]]</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=6iru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iru OCA], [http://pdbe.org/6iru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iru RCSB], [http://www.ebi.ac.uk/pdbsum/6iru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iru ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Peptidase E (PepE) is a nonclassical serine peptidase with a Ser-His-Glu catalytic triad. It is specific for dipeptides with an N-terminal aspartate residue (Asp-X dipeptidase activity). Its homolog from Listeria monocytogenes (PepElm) has a Ser-His-Asn "catalytic triad." Based on sequence alignment we predicted that the PepE homolog from Deinococcus radiodurans (PepEdr) would have a Ser-His-Asp "catalytic triad." We confirmed this by solving the crystal structure of PepEdr to 2.7 A resolution. We show that PepElm and PepEdr lack the Asp-X dipeptidase activity. Our analyses suggest that absence of P1 pocket in the active site could be the main reason for this lack of typical activity. Sequence and structural data reveal that the PepE homologs can be divided into long and short PepEs based on presence or absence of a C-terminal tail which adopts a beta-hairpin conformation in the canonical PepE from Salmonella enterica. A long PepE from Bacillus subtilis with Ser-His-Asp catalytic triad exhibits Asp-X dipeptidase activity. Whereas the three long PepEs enzymatically characterized till date have been found to possess the Asp-X dipeptidase activity, the three enzymatically characterized short PepEs lack this activity irrespective of the nature of their catalytic triads. This study illuminates the structural and functional heterogeneity in the S51 family and also provides structural basis for the functional variability among PepE homologs.

-	~~Authors~~: ~~Yadav~~, P., ~~Chandravanshi~~, K., Kumar, A., ~~Makde~~, R.D.	+	Catalytic triad heterogeneity in S51 peptidase family: Structural basis for functional variability.,Yadav P, Goyal VD, Chandravanshi K, Kumar A, Gokhale SM, Jamdar SN, Makde RD Proteins. 2019 Aug;87(8):679-692. doi: 10.1002/prot.25693. Epub 2019 May 3. PMID:30968972<ref>PMID:30968972</ref>

-	~~Description: Crystal structure~~ of ~~Peptidase E from Deinococcus radiodurans in P6422 space group~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Makde, R.D]]~~	+	<div class="pdbe-citations 6iru" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Kumar, A~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Chandravanshi, K]]		[[Category: Chandravanshi, K]]
		+	[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
	[[Category: Yadav, P]]		[[Category: Yadav, P]]
		+	[[Category: Active site]]
		+	[[Category: Dimer]]
		+	[[Category: Esterase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Peptidase e]]
		+	[[Category: S51 peptidase]]

OCA at 05:09, 5 December 2018

2018-12-05T05:09:12Z

←Older revision		Revision as of 05:09, 5 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Yadav, P., Chandravanshi, K., Kumar, A., Makde, R.D.		Authors: Yadav, P., Chandravanshi, K., Kumar, A., Makde, R.D.
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	Description: Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group		Description: Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chandravanshi, K]]
	[[Category: Makde, R.D]]		[[Category: Makde, R.D]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
		+	[[Category: Chandravanshi, K]]
	[[Category: Yadav, P]]		[[Category: Yadav, P]]

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

2018-12-02T18:54:18Z

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

←Older revision

Revision as of 18:54, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6iru is ON HOLD Authors: Yadav, P., Chandravanshi, K., Kumar, A., Makde, R.D. Description: Crystal structure of Peptidase E from Deinococcus radiod...

2018-12-02T18:54:17Z

New page: '''Unreleased structure''' The entry 6iru is ON HOLD Authors: Yadav, P., Chandravanshi, K., Kumar, A., Makde, R.D. Description: Crystal structure of Peptidase E from Deinococcus radiod...

New page

'''Unreleased structure'''

The entry 6iru is ON HOLD

Authors: Yadav, P., Chandravanshi, K., Kumar, A., Makde, R.D.

Description: Crystal structure of Peptidase E from Deinococcus radiodurans in P6422 space group
[[Category: Unreleased Structures]]
[[Category: Chandravanshi, K]]
[[Category: Makde, R.D]]
[[Category: Kumar, A]]
[[Category: Yadav, P]]