5ypd - Revision history

OCA at 08:34, 22 November 2023

OCA — Wed, 22 Nov 2023 08:34:50 GMT

←Older revision		Revision as of 08:34, 22 November 2023
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	<StructureSection load='5ypd' size='340' side='right'caption='[[5ypd]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='5ypd' size='340' side='right'caption='[[5ypd]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycta Mycta~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YPD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.62Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mapB, map, MRA_2886 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] </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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [https://pdbe.org/5ypd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [https://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd 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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [~~http~~://pdbe.org/5ypd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5U6L5_MYCTA A5U6L5_MYCTA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Methionyl aminopeptidase]]~~	+	[[Category: Mycobacterium tuberculosis H37Ra]]
-	~~[[Category: Mycta~~]]	+	[[Category: Addlagatta A]]
-	[[Category: Addlagatta, A]]	+	[[Category: Sandeep CB]]
-	[[Category: Sandeep~~, C B]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Methionine aminopeptidase~~]]	+

OCA at 07:48, 11 March 2020

OCA — Wed, 11 Mar 2020 07:48:37 GMT

←Older revision		Revision as of 07:48, 11 March 2020
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	<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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [http://pdbe.org/5ypd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [http://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd 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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [http://pdbe.org/5ypd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [http://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methionine aminopeptidases (MetAPs) are a class of enzymes evolved to cleave initiator methionine in 60-70% of the total cellular proteins in all living cells. Based on their sequence differences, they are classified into Type 1 and Type 2. Type 1 is further divided into Type 1a, 1a', 1b, 1c and 1d. Irrespective of various classifications, all MetAPs reported till date displayed hydrolytic activity against peptides that contain only methionine on the N-terminus. A cysteine at the top of the active site in all the Type 1 structures is reported to be critical for the specificity. Mutation of this cysteine to serine or asparagine leads to loss of specificity. In the present study, we have identified a class of MetAPs in some of the proteobacteria that have an asparagine at this site. Most of the proteobacteria that contain MetAP1n are pathogenic in nature. Biochemical and structural studies on two proteins, one from each of V. coralliilyticus and K. pneumoniae confirm that these enzymes cleave leucine in addition to methionine. Crystallographic and homology modeling studies suggest that relaxed substrate specificity of this new class of enzymes could be due to the increased flexibility in the active site. Since this new class has an asparagine at the critical position that probably contributes for the relaxed substrate specificity and also differentiates them from other Type 1 MetAPs, we classified them as Type 1n.
		+
		+	Discovery of a new class of type 1 methionine aminopeptidases that have relaxed substrate specificity.,Bala SC, Haque N, Pillalamarri V, Reddi R, Kashyap R, Marapaka AK, Addlagatta A Int J Biol Macromol. 2019 May 15;129:523-529. doi:, 10.1016/j.ijbiomac.2019.02.055. Epub 2019 Feb 11. PMID:30763644<ref>PMID:30763644</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ypd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]		*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:06, 20 November 2019

OCA — Wed, 20 Nov 2019 17:06:03 GMT

←Older revision		Revision as of 17:06, 20 November 2019
Line 1:		Line 1:

	==Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine==		==Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine==
-	<StructureSection load='5ypd' size='340' side='right' caption='[[5ypd]], [[Resolution\|resolution]] 1.62Å' scene=''>	+	<StructureSection load='5ypd' size='340' side='right'caption='[[5ypd]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mapB, map, MRA_2886 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] </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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [http://pdbe.org/5ypd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [http://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd 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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [http://pdbe.org/5ypd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [http://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd ProSAT]</span></td></tr>
	</table>		</table>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
		+	[[Category: Mycta]]
	[[Category: Addlagatta, A]]		[[Category: Addlagatta, A]]
	[[Category: Sandeep, C B]]		[[Category: Sandeep, C B]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Methionine aminopeptidase]]		[[Category: Methionine aminopeptidase]]

OCA at 12:08, 7 November 2018

OCA — Wed, 07 Nov 2018 12:08:20 GMT

←Older revision		Revision as of 12:08, 7 November 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5ypd is ON HOLD until Paper Publication~~	+	==Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine==
-		+	<StructureSection load='5ypd' size='340' side='right' caption='[[5ypd]], [[Resolution\|resolution]] 1.62Å' scene=''>
-	~~Authors: Sandeep, C.B., Addlagatta, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ypd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPD FirstGlance]. <br>
-	~~Description:~~ Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18] </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=5ypd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ypd OCA], [http://pdbe.org/5ypd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ypd RCSB], [http://www.ebi.ac.uk/pdbsum/5ypd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ypd ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Methionyl aminopeptidase]]
	[[Category: Addlagatta, A]]		[[Category: Addlagatta, A]]
-	[[Category: Sandeep, C.B]]	+	[[Category: Sandeep, C B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Methionine aminopeptidase]]

OCA: Protected "5ypd" [edit=sysop:move=sysop]

OCA — Wed, 08 Nov 2017 06:28:45 GMT

Protected "5ypd" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:28, 8 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ypd is ON HOLD until Paper Publication Authors: Sandeep, C.B., Addlagatta, A. Description: Mycobacterium Tuberculosis Methionine aminopeptidase ty...

OCA — Wed, 08 Nov 2017 06:28:44 GMT

New page: '''Unreleased structure''' The entry 5ypd is ON HOLD until Paper Publication Authors: Sandeep, C.B., Addlagatta, A. Description: Mycobacterium Tuberculosis Methionine aminopeptidase ty...

New page

'''Unreleased structure'''

The entry 5ypd is ON HOLD until Paper Publication

Authors: Sandeep, C.B., Addlagatta, A.

Description: Mycobacterium Tuberculosis Methionine aminopeptidase type 1c (C105N mutant) in complex with Methionine
[[Category: Unreleased Structures]]
[[Category: Addlagatta, A]]
[[Category: Sandeep, C.B]]