6ifg - Revision history

OCA at 09:40, 22 November 2023

OCA — Wed, 22 Nov 2023 09:40:44 GMT

←Older revision		Revision as of 09:40, 22 November 2023
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	<StructureSection load='6ifg' size='340' side='right'caption='[[6ifg]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6ifg' size='340' side='right'caption='[[6ifg]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ifg]] 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=6IFG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IFG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ifg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus Deinococcus] and [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=6IFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IFG FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=FMT:FORMIC+ACID'>FMT</scene~~>, ~~<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]] 1.9Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~DR_0875 ([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=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6ifg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ifg OCA], [~~http~~://pdbe.org/6ifg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ifg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ifg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ifg 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=6ifg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ifg OCA], [https://pdbe.org/6ifg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ifg RCSB], [https://www.ebi.ac.uk/pdbsum/6ifg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ifg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RVZ5_DEIRA Q9RVZ5_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: ~~Deira~~]]	+	[[Category: Deinococcus]]
		+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Agrawal, R]]	+	[[Category: Agrawal R]]
-	[[Category: Kumar, A]]	+	[[Category: Kumar A]]
-	[[Category: Makde~~, R D]]~~	+	[[Category: Makde RD]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metalloprotease]]~~	+
-	~~[[Category: Peptidase~~]]	+

OCA at 17:26, 20 November 2019

OCA — Wed, 20 Nov 2019 17:26:50 GMT

←Older revision		Revision as of 17:26, 20 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6ifg is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans==
		+	<StructureSection load='6ifg' size='340' side='right'caption='[[6ifg]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ifg]] 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=6IFG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DR_0875 ([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=6ifg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ifg OCA], [http://pdbe.org/6ifg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ifg RCSB], [http://www.ebi.ac.uk/pdbsum/6ifg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ifg ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Zinc metallopeptidases of the M1 family (M1 peptidases) with unique metal binding motif HEXXH(X)18E regulate many important biological processes such as tumor growth, angiogenesis, hormone regulation, and immune cell development. Typically, these enzymes exist in three-domain [N-terminal domain (N-domain), catalytic domain, and C-terminal domain (C-domain)] or four-domain (N-domain, catalytic domain, middle domain, and C-domain) format in which N-domain and catalytic domain are more conserved. The C-domain plays important roles in substrate binding and gating. In this study we report the first structure of a two-domain (N-domain and catalytic domain) M1 peptidase at 2.05A resolution. Despite the lack of C-domain, the enzyme is active and prefers peptide substrates with large hydrophobic N-terminal residues. Its substrate-bound structure was determined at 1.9A resolution. Structural analyses supported by site directed mutagenesis and molecular dynamics simulations reveal structural features that could compensate for the lack of C-domain. A unique loop insertion (loop A) in the N-domain has important roles in gating and desolvation of active site. Three Arg residues of the catalytic domain are involved in substrate-binding roles typically played by positively charged residues of C-domain in other M1 peptidases. Further, its unique exopeptidase sequence motif, LALET, creates a more hydrophobic environment at the S1 subsite (which binds N-terminal residue of the substrate in aminopeptidases) than the more common GXMEN motif in the family. This leads to high affinity for large hydrophobic residues in the S1 subsite, which contributes towards efficient substrate binding in absence of C-domain.

-	~~Authors~~: ~~Agrawal~~, R., ~~Kumar~~, A., ~~Kumar~~, A., Makde~~, R~~.D.	+	Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain.,Agrawal R, Goyal VD, Kumar A, Gaur NK, Jamdar SN, Kumar A, Makde RD J Struct Biol. 2019 Oct 1;208(1):51-60. doi: 10.1016/j.jsb.2019.07.010. Epub 2019, Jul 25. PMID:31351924<ref>PMID:31351924</ref>

-	~~Description: Crystal structure~~ of ~~M1 zinc metallopeptidase E323A mutant bound to Tyr~~-~~ser~~-~~ala substrate from Deinococcus radiodurans~~	+	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 6ifg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deira]]
		+	[[Category: Large Structures]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metalloprotease]]
		+	[[Category: Peptidase]]

OCA at 10:41, 7 November 2018

OCA — Wed, 07 Nov 2018 10:41:03 GMT

←Older revision		Revision as of 10:41, 7 November 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ifg is ON HOLD	+	The entry 6ifg 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: Protected "6ifg" [edit=sysop:move=sysop]

OCA — Wed, 26 Sep 2018 06:23:05 GMT

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

←Older revision

Revision as of 06:23, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6ifg is ON HOLD Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D. Description: Crystal structure of M1 zinc metallopeptidase E323A mutant bou...

OCA — Wed, 26 Sep 2018 06:23:04 GMT

New page: '''Unreleased structure''' The entry 6ifg is ON HOLD Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D. Description: Crystal structure of M1 zinc metallopeptidase E323A mutant bou...

New page

'''Unreleased structure'''

The entry 6ifg is ON HOLD

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

Description: Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans
[[Category: Unreleased Structures]]
[[Category: Makde, R.D]]
[[Category: Agrawal, R]]
[[Category: Kumar, A]]