6a8z - Revision history

OCA at 09:21, 22 November 2023

2023-11-22T09:21:24Z

←Older revision		Revision as of 09:21, 22 November 2023
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	<StructureSection load='6a8z' size='340' side='right'caption='[[6a8z]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6a8z' size='340' side='right'caption='[[6a8z]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a8z]] 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=6A8Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6A8Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a8z]] 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=6A8Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A8Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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]] 2.045Å</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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=6a8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8z OCA], [~~http~~://pdbe.org/6a8z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6a8z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6a8z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8z 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=6a8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8z OCA], [https://pdbe.org/6a8z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a8z RCSB], [https://www.ebi.ac.uk/pdbsum/6a8z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8z 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 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 17:07, 20 November 2019

2019-11-20T17:07:49Z

←Older revision		Revision as of 17:07, 20 November 2019
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	<StructureSection load='6a8z' size='340' side='right'caption='[[6a8z]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6a8z' size='340' side='right'caption='[[6a8z]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6a8z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A8Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6a8z]] 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=6A8Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A8Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</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=6a8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8z OCA], [http://pdbe.org/6a8z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a8z RCSB], [http://www.ebi.ac.uk/pdbsum/6a8z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8z 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=6a8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8z OCA], [http://pdbe.org/6a8z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a8z RCSB], [http://www.ebi.ac.uk/pdbsum/6a8z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8z ProSAT]</span></td></tr>
	</table>		</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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6a8z" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]

OCA at 10:35, 17 July 2019

2019-07-17T10:35:34Z

←Older revision		Revision as of 10:35, 17 July 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6a8z ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of M1 zinc metallopeptidase from Deinococcus radiodurans==
-		+	<StructureSection load='6a8z' size='340' side='right'caption='[[6a8z]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6a8z]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A8Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A8Z FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TYR:TYROSINE'>TYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6a8z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a8z OCA], [http://pdbe.org/6a8z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a8z RCSB], [http://www.ebi.ac.uk/pdbsum/6a8z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a8z ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Agrawal, R]]
		+	[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metalloprotease]]
		+	[[Category: Peptidase]]

OCA at 04:33, 22 August 2018

2018-08-22T04:33:04Z

←Older revision		Revision as of 04:33, 22 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6a8z is ON HOLD	+	The entry 6a8z is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6a8z" [edit=sysop:move=sysop]

2018-07-18T05:13:23Z

Protected "6a8z" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 18 July 2018

OCA: New page: '''Unreleased structure''' The entry 6a8z is ON HOLD Authors: Description: Category: Unreleased Structures

2018-07-18T05:13:20Z

New page: '''Unreleased structure''' The entry 6a8z is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6a8z is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]