3pka - Revision history

OCA at 10:41, 21 February 2024

OCA — Wed, 21 Feb 2024 10:41:24 GMT

←Older revision		Revision as of 10:41, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3pka' size='340' side='right'caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='3pka' size='340' side='right'caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PKA FirstGlance]. <br>
-	</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</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]] 1.25Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</div></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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [https://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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [https://pdbe.org/3pka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [https://www.ebi.ac.uk/pdbsum/3pka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pka 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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [https://pdbe.org/3pka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [https://www.ebi.ac.uk/pdbsum/3pka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~AMPM2_MYCTU AMPM2_MYCTU]~~] Removes the N-terminal methionine from nascent proteins~~, when the penultimate amino acid is alanine or proline, but enzyme activity~~ is ~~remarkably low~~ when the second residue ~~is phenylalanine or leucine. With glycine at~~ the ~~second position, Map~~ is ~~more active with a tetrapeptide than with a tripeptide.<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>~~	+	[https://www.uniprot.org/uniprot/MAP12_MYCTU MAP12_MYCTU] Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed.[HAMAP-Rule:MF_01974]<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Methionine aminopeptidase~~ (~~MetAP) carries out an essential function of protein N~~-terminal processing in many bacteria and is a promising target for the development of novel antitubercular agents. Natural bengamides potently inhibit the proliferation of mammalian cells by targeting MetAP enzymes, and the X-ray crystal structure of human type 2 MetAP in complex with a bengamide derivative reveals the key interactions at the active site. By preserving the interactions with the conserved residues inside the binding pocket while exploring the differences between bacterial and human MetAPs around the binding pocket, ~~seven bengamide derivatives were synthesized and evaluated for inhibition of MtMetAP1a and MtMetAP1c in different metalloforms~~, ~~inhibition of M. tuberculosis growth in replicating and non-replicating states~~, and inhibition of human K562 cell growth. Potent inhibition of MtMetAP1a and MtMetAP1c and modest growth inhibition of M. tuberculosis were observed for some of these derivatives. Crystal structures of MtMetAP1c in complex with two of the derivatives provided valuable structural information for improvement of these inhibitors for potency and selectivity.	+
-		+
-	~~Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.~~,~~Lu JP~~, ~~Yuan XH~~, ~~Yuan H, Wang WL, Wan B, Franzblau SG, Ye QZ ChemMedChem~~. ~~2011 Apr 4~~. ~~doi~~: ~~10.1002/cmdc.201100003. PMID:21465667~~<ref>PMID:~~21465667~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3pka" style="background-color~~:~~#fffaf0;">~~</~~div~~>	+

	==See Also==		==See Also==
Line 29:		Line 18:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Methionyl aminopeptidase~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: Lu~~, J P~~]]	+	[[Category: Lu JP]]
-	[[Category: Ye~~, Q Z]]~~	+	[[Category: Ye QZ]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex~~]]	+

OCA at 08:43, 25 May 2022

OCA — Wed, 25 May 2022 08:43:07 GMT

←Older revision		Revision as of 08:43, 25 May 2022
Line 1:		Line 1:

	==M. tuberculosis MetAP with bengamide analog Y02, in Mn form==		==M. tuberculosis MetAP with bengamide analog Y02, in Mn form==
-	<StructureSection load='3pka' size='340' side='right' caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>	+	<StructureSection load='3pka' size='340' side='right'caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3PKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PKA 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</scene></td></tr>	+	</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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'>[https://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [https://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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [~~http~~://pdbe.org/3pka PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3pka PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3pka 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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [https://pdbe.org/3pka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [https://www.ebi.ac.uk/pdbsum/3pka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AMPM2_MYCTU AMPM2_MYCTU]] Removes the N-terminal methionine from nascent proteins, when the penultimate amino acid is alanine or proline, but enzyme activity is remarkably low when the second residue is phenylalanine or leucine. With glycine at the second position, Map is more active with a tetrapeptide than with a tripeptide.<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>	+	[[https://www.uniprot.org/uniprot/AMPM2_MYCTU AMPM2_MYCTU]] Removes the N-terminal methionine from nascent proteins, when the penultimate amino acid is alanine or proline, but enzyme activity is remarkably low when the second residue is phenylalanine or leucine. With glycine at the second position, Map is more active with a tetrapeptide than with a tripeptide.<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Aminopeptidase\|Aminopeptidase]]	+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
	[[Category: Lu, J P]]		[[Category: Lu, J P]]
	[[Category: Ye, Q Z]]		[[Category: Ye, Q Z]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 14:58, 5 August 2016

OCA — Fri, 05 Aug 2016 14:58:36 GMT

←Older revision		Revision as of 14:58, 5 August 2016
Line 1:		Line 1:
		+
	==M. tuberculosis MetAP with bengamide analog Y02, in Mn form==		==M. tuberculosis MetAP with bengamide analog Y02, in Mn form==
	<StructureSection load='3pka' size='340' side='right' caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='3pka' size='340' side='right' caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PKA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PKA 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 ~~Mycobacterium~~ tuberculosis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [http://www.ebi.ac.uk/pdbsum/3pka PDBsum]</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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [http://pdbe.org/3pka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [http://www.ebi.ac.uk/pdbsum/3pka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pka ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3pka" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Lu, J P]]		[[Category: Lu, J P]]
	[[Category: Ye, Q Z]]		[[Category: Ye, Q Z]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 03:27, 25 December 2014

OCA — Thu, 25 Dec 2014 03:27:04 GMT

←Older revision		Revision as of 03:27, 25 December 2014
Line 9:		Line 9:
	<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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [http://www.ebi.ac.uk/pdbsum/3pka PDBsum]</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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [http://www.ebi.ac.uk/pdbsum/3pka PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPM2_MYCTU AMPM2_MYCTU]] Removes the N-terminal methionine from nascent proteins, when the penultimate amino acid is alanine or proline, but enzyme activity is remarkably low when the second residue is phenylalanine or leucine. With glycine at the second position, Map is more active with a tetrapeptide than with a tripeptide.<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 10:41, 19 December 2014

OCA — Fri, 19 Dec 2014 10:41:09 GMT

←Older revision		Revision as of 10:41, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3pka\| PDB=3pka \| SCENE= }}~~	+	==M. tuberculosis MetAP with bengamide analog Y02, in Mn form==
-	===M. tuberculosis MetAP with bengamide analog Y02, in Mn form===	+	<StructureSection load='3pka' size='340' side='right' caption='[[3pka]], [[Resolution\|resolution]] 1.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21465667}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PKA 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Y02:(2R,3R,4S,5R,6E)-3,4,5-TRIHYDROXY-2-METHOXY-8,8-DIMETHYL-N-[2-(2,4,6-TRIMETHYLPHENOXY)ETHYL]NON-6-ENAMIDE'>Y02</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iu7\|3iu7]], [[3iu8\|3iu8]], [[3iu9\|3iu9]], [[3pke\|3pke]], [[3pkb\|3pkb]], [[3pkc\|3pkc]], [[3pkd\|3pkd]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">map, mapB, MT2929, MTV003.07c, Rv2861c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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=3pka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pka OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3pka RCSB], [http://www.ebi.ac.uk/pdbsum/3pka PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methionine aminopeptidase (MetAP) carries out an essential function of protein N-terminal processing in many bacteria and is a promising target for the development of novel antitubercular agents. Natural bengamides potently inhibit the proliferation of mammalian cells by targeting MetAP enzymes, and the X-ray crystal structure of human type 2 MetAP in complex with a bengamide derivative reveals the key interactions at the active site. By preserving the interactions with the conserved residues inside the binding pocket while exploring the differences between bacterial and human MetAPs around the binding pocket, seven bengamide derivatives were synthesized and evaluated for inhibition of MtMetAP1a and MtMetAP1c in different metalloforms, inhibition of M. tuberculosis growth in replicating and non-replicating states, and inhibition of human K562 cell growth. Potent inhibition of MtMetAP1a and MtMetAP1c and modest growth inhibition of M. tuberculosis were observed for some of these derivatives. Crystal structures of MtMetAP1c in complex with two of the derivatives provided valuable structural information for improvement of these inhibitors for potency and selectivity.

-	~~==Function==~~	+	Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.,Lu JP, Yuan XH, Yuan H, Wang WL, Wan B, Franzblau SG, Ye QZ ChemMedChem. 2011 Apr 4. doi: 10.1002/cmdc.201100003. PMID:21465667<ref>PMID:21465667</ref>
-	~~[[http://www~~.~~uniprot.org/uniprot/AMPM2_MYCTU AMPM2_MYCTU]] Removes the N-terminal methionine from nascent proteins~~, ~~when the penultimate amino acid is alanine or proline~~, ~~but enzyme activity is remarkably low when the second residue is phenylalanine or leucine. With glycine at the second position~~, ~~Map is more active with a tetrapeptide than with a tripeptide~~.~~<ref>~~PMID:~~19688379</ref>~~ <ref>PMID:~~20038112~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3pka]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:021465667</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Aminopeptidase\|Aminopeptidase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Lu, J P.]]	+	[[Category: Lu, J P]]
-	[[Category: Ye, Q Z.]]	+	[[Category: Ye, Q Z]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA at 16:26, 19 June 2013

OCA — Wed, 19 Jun 2013 16:26:45 GMT

←Older revision		Revision as of 16:26, 19 June 2013
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-	[[Image:3pka.png\|left\|200px]]
-
	{{STRUCTURE_3pka\| PDB=3pka \| SCENE= }}		{{STRUCTURE_3pka\| PDB=3pka \| SCENE= }}
-
	===M. tuberculosis MetAP with bengamide analog Y02, in Mn form===		===M. tuberculosis MetAP with bengamide analog Y02, in Mn form===
-
	{{ABSTRACT_PUBMED_21465667}}		{{ABSTRACT_PUBMED_21465667}}
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/AMPM2_MYCTU AMPM2_MYCTU]] Removes the N-terminal methionine from nascent proteins, when the penultimate amino acid is alanine or proline, but enzyme activity is remarkably low when the second residue is phenylalanine or leucine. With glycine at the second position, Map is more active with a tetrapeptide than with a tripeptide.<ref>PMID:19688379</ref> <ref>PMID:20038112</ref>

	==About this Structure==		==About this Structure==
	[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].		[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].
-
-	==See Also==
-	*[[Aminopeptidase\|Aminopeptidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:021465667</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021465667</ref><references group="xtra"/><references/>
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]

OCA at 12:08, 20 October 2012

OCA — Sat, 20 Oct 2012 12:08:35 GMT

←Older revision		Revision as of 12:08, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3pka]] is a 1 chain structure ~~of [[Aminopeptidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].	+	[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].

	==See Also==		==See Also==

OCA at 07:45, 26 July 2012

OCA — Thu, 26 Jul 2012 07:45:41 GMT

←Older revision		Revision as of 07:45, 26 July 2012
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	[[Image:3pka.png\|left\|200px]]		[[Image:3pka.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3pka\| PDB=3pka \| SCENE= }}		{{STRUCTURE_3pka\| PDB=3pka \| SCENE= }}

	===M. tuberculosis MetAP with bengamide analog Y02, in Mn form===		===M. tuberculosis MetAP with bengamide analog Y02, in Mn form===

-
-	<!--
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	==See Also==		==See Also==
-	*[[Aminopeptidase]]	+	*[[Aminopeptidase\|Aminopeptidase]]

	==Reference==		==Reference==

OCA at 08:01, 13 July 2011

OCA — Wed, 13 Jul 2011 08:01:05 GMT

←Older revision		Revision as of 08:01, 13 July 2011
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-	[[Image:3pka.~~jpg~~\|left\|200px]]	+	[[Image:3pka.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	[[3pka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].	+	[[3pka]] is a 1 chain structure of [[Aminopeptidase]] with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PKA OCA].
		+
		+	==See Also==
		+	*[[Aminopeptidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21465667~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021465667</ref><references group="xtra"/>
	[[Category: Methionyl aminopeptidase]]		[[Category: Methionyl aminopeptidase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Lu, J P.]]		[[Category: Lu, J P.]]
	[[Category: Ye, Q Z.]]		[[Category: Ye, Q Z.]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]

OCA: Protected "3pka" [edit=sysop:move=sysop]

OCA — Thu, 21 Apr 2011 10:36:20 GMT

Protected "3pka" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:36, 21 April 2011