6kp0 - Revision history

OCA at 10:38, 22 November 2023

OCA — Wed, 22 Nov 2023 10:38:46 GMT

←Older revision		Revision as of 10:38, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kp0' size='340' side='right'caption='[[6kp0]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6kp0' size='340' side='right'caption='[[6kp0]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kp0]] 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=6KP0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KP0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kp0]] 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=6KP0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KP0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.1Å</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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp0 OCA], [~~http~~://pdbe.org/6kp0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kp0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kp0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp0 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=6kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp0 OCA], [https://pdbe.org/6kp0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kp0 RCSB], [https://www.ebi.ac.uk/pdbsum/6kp0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp0 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 ==
Line 21:		Line 23:
	__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~~]]	+

OCA at 08:59, 5 February 2020

OCA — Wed, 05 Feb 2020 08:59:13 GMT

←Older revision		Revision as of 08:59, 5 February 2020
Line 3:		Line 3:
	<StructureSection load='6kp0' size='340' side='right'caption='[[6kp0]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6kp0' size='340' side='right'caption='[[6kp0]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kp0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KP0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kp0]] 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=6KP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KP0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp0 OCA], [http://pdbe.org/6kp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp0 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=6kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp0 OCA], [http://pdbe.org/6kp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp0 ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deira]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]

OCA at 16:09, 22 January 2020

OCA — Wed, 22 Jan 2020 16:09:05 GMT

←Older revision		Revision as of 16:09, 22 January 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kp0 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine==
		+	<StructureSection load='6kp0' size='340' side='right'caption='[[6kp0]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kp0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KP0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KP0 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6kp0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp0 OCA], [http://pdbe.org/6kp0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp0 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp0 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	M1 metallopeptidases regulate many important biological processes such as angiogenesis, tumour growth, hormone regulation, and immune cell development. Knowledge of substrate specificity mechanism in this family is valuable. An M1 peptidase from Deinococcus radiodurans (M1dr) with preference for bulky hydrophobic residues at N-terminus of peptide substrates was recently reported. In contrast to Escherichia coli aminopeptidase N, a previously characterized M1 peptidase, M1dr exhibits reduced activity towards peptides with N-terminal Arg or Ala residue. In order to illuminate structural basis of substrate specificity, we report several crystal structures of M1dr with different amino acids bound to the active site. Structural analysis indicated that the enzyme makes subtle adjustments to multiple residues leading to significant volume change of the active site cavity to accommodate residues of varying sizes (Leu to Trp). This study further reveals that the low preference for Arg at N-terminus of peptide substrate arises from a non-productive conformation in which many of the Arg molecules bind where they block the proton donor essential for the peptidase reaction. Hence, this study illuminates the substrate-binding mechanism and also reveals the structural basis for the substrate specificity of M1dr enzyme.

-	~~Authors:~~ Agrawal, R., Kumar, A., ~~Kumar~~, A., Makde~~, R~~.D.	+	Structural basis for the unusual substrate specificity of unique two-domain M1 metallopeptidase.,Agrawal R, Goyal VD, Singh R, Kumar A, Jamdar SN, Kumar A, Makde RD Int J Biol Macromol. 2020 Jan 7;147:304-313. doi: 10.1016/j.ijbiomac.2019.12.239. PMID:31923495<ref>PMID:31923495</ref>

-	~~Description: Crystal structure~~ of ~~two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine~~	+	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 6kp0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Agrawal, R]]		[[Category: Agrawal, R]]
	[[Category: Kumar, A]]		[[Category: Kumar, A]]
		+	[[Category: Makde, R D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metalloprotease]]

OCA at 06:37, 2 October 2019

OCA — Wed, 02 Oct 2019 06:37:03 GMT

←Older revision		Revision as of 06:37, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kp0 is ON HOLD	+	The entry 6kp0 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 "6kp0" [edit=sysop:move=sysop]

OCA — Wed, 21 Aug 2019 04:05:04 GMT

Protected "6kp0" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 21 August 2019

OCA: New page: '''Unreleased structure''' The entry 6kp0 is ON HOLD Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D. Description: Crystal structure of two domain M1 zinc metallopeptidase E323A...

OCA — Wed, 21 Aug 2019 04:05:03 GMT

New page: '''Unreleased structure''' The entry 6kp0 is ON HOLD Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D. Description: Crystal structure of two domain M1 zinc metallopeptidase E323A...

New page

'''Unreleased structure'''

The entry 6kp0 is ON HOLD

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

Description: Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-arginine
[[Category: Unreleased Structures]]
[[Category: Makde, R.D]]
[[Category: Agrawal, R]]
[[Category: Kumar, A]]