6kp1 - Revision history

OCA at 10:38, 22 November 2023

OCA — Wed, 22 Nov 2023 10:38:47 GMT

←Older revision		Revision as of 10:38, 22 November 2023
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	<StructureSection load='6kp1' size='340' side='right'caption='[[6kp1]], [[Resolution\|resolution]] 2.19Å' scene=''>		<StructureSection load='6kp1' size='340' side='right'caption='[[6kp1]], [[Resolution\|resolution]] 2.19Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kp1]] 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=6KP1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KP1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kp1]] 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=6KP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KP1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MET:METHIONINE'>MET</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]] 2.19Å</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=MET:METHIONINE'>MET</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~~://proteopedia.org/fgij/fg.htm?mol=6kp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp1 OCA], [~~http~~://pdbe.org/6kp1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kp1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kp1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp1 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=6kp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp1 OCA], [https://pdbe.org/6kp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kp1 RCSB], [https://www.ebi.ac.uk/pdbsum/6kp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp1 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~~]]	+

OCA at 12:40, 16 December 2020

OCA — Wed, 16 Dec 2020 12:40:43 GMT

←Older revision		Revision as of 12:40, 16 December 2020
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	==Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine amino acid==		==Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine amino acid==
-	<StructureSection load='6kp1' size='340' side='right'caption='[[6kp1]]' scene=''>	+	<StructureSection load='6kp1' size='340' side='right'caption='[[6kp1]], [[Resolution\|resolution]] 2.19Å' 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=6KP1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KP1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kp1]] 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=6KP1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KP1 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=6kp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp1 OCA], [http://pdbe.org/6kp1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp1 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=MET:METHIONINE'>MET</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://proteopedia.org/fgij/fg.htm?mol=6kp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp1 OCA], [http://pdbe.org/6kp1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp1 ProSAT]</span></td></tr>
	</table>		</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.
		+
		+	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>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kp1" 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]]
-	[[Category: Kumar A]]	+	[[Category: Kumar, A]]
-	[[Category: Makde RD]]	+	[[Category: Makde, R D]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metalloprotease]]

OCA at 06:15, 25 June 2020

OCA — Thu, 25 Jun 2020 06:15:49 GMT

←Older revision		Revision as of 06:15, 25 June 2020
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-	'''Unreleased structure'''

-	~~The entry 6kp1 is ON HOLD until Paper Publication~~	+	==Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine amino acid==
-		+	<StructureSection load='6kp1' size='340' side='right'caption='[[6kp1]]' scene=''>
-	~~Authors: Agrawal, R., Kumar, A., Kumar, A., Makde, R.D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KP1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KP1 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of two domain M1 zinc metallopeptidase E323A mutant bound to L-methionine amino acid	+	</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=6kp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kp1 OCA], [http://pdbe.org/6kp1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kp1 RCSB], [http://www.ebi.ac.uk/pdbsum/6kp1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kp1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Makde~~, R.D]]	+	__TOC__
-	[[Category: Agrawal, R]]	+	</StructureSection>
-	[[Category: Kumar, A]]	+	[[Category: Large Structures]]
		+	[[Category: Agrawal R]]
		+	[[Category: Kumar A]]
		+	[[Category: Makde RD]]

OCA at 06:37, 2 October 2019

OCA — Wed, 02 Oct 2019 06:37:07 GMT

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

-	The entry 6kp1 is ON HOLD	+	The entry 6kp1 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 "6kp1" [edit=sysop:move=sysop]

OCA — Wed, 21 Aug 2019 04:05:08 GMT

Protected "6kp1" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:05, 21 August 2019

OCA: New page: '''Unreleased structure''' The entry 6kp1 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 04:05:06 GMT

New page: '''Unreleased structure''' The entry 6kp1 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 6kp1 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-methionine amino acid
[[Category: Unreleased Structures]]
[[Category: Makde, R.D]]
[[Category: Agrawal, R]]
[[Category: Kumar, A]]