5ntd - Revision history

OCA at 12:07, 22 November 2023

2023-11-22T12:07:29Z

←Older revision		Revision as of 12:07, 22 November 2023
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	==Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin==		==Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin==
-	<StructureSection load='5ntd' size='340' side='right' caption='[[5ntd]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5ntd' size='340' side='right'caption='[[5ntd]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ntd]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Trybb Trybb~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NTD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ntd]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NTD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb11.02.4440 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ntd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntd OCA], [~~http~~://pdbe.org/5ntd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ntd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ntd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntd 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=5ntd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntd OCA], [https://pdbe.org/5ntd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ntd RCSB], [https://www.ebi.ac.uk/pdbsum/5ntd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q385B0_TRYB2 Q385B0_TRYB2]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Aminopeptidase\|Aminopeptidase]]	+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Trybb~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Timm, J~~]]	+	[[Category: Trypanosoma brucei brucei]]
-	[[Category: ~~Wilson, K~~]]	+	[[Category: Timm J]]
-	[[Category: ~~Aminopeptidase]]~~	+	[[Category: Wilson K]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: M17 leucyl aminopeptidase]]~~	+
-	~~[[Category: Tryanosoma brucei bestatin~~]]	+

OCA at 07:01, 28 March 2018

2018-03-28T07:01:08Z

←Older revision		Revision as of 07:01, 28 March 2018
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	</div>		</div>
	<div class="pdbe-citations 5ntd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ntd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase\|Aminopeptidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:45, 22 February 2018

2018-02-22T07:45:13Z

←Older revision		Revision as of 07:45, 22 February 2018
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	<StructureSection load='5ntd' size='340' side='right' caption='[[5ntd]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5ntd' size='340' side='right' caption='[[5ntd]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ntd]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NTD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ntd]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Trybb Trybb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NTD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tb11.02.4440 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5702 TRYBB])</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=5ntd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntd OCA], [http://pdbe.org/5ntd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ntd RCSB], [http://www.ebi.ac.uk/pdbsum/5ntd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntd 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=5ntd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntd OCA], [http://pdbe.org/5ntd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ntd RCSB], [http://www.ebi.ac.uk/pdbsum/5ntd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntd ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Trybb]]
	[[Category: Timm, J]]		[[Category: Timm, J]]
	[[Category: Wilson, K]]		[[Category: Wilson, K]]

OCA at 04:18, 30 August 2017

2017-08-30T04:18:39Z

←Older revision		Revision as of 04:18, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ntd is ~~ON HOLD until Paper~~ Publication	+	==Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin==
		+	<StructureSection load='5ntd' size='340' side='right' caption='[[5ntd]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ntd]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NTD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NTD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=BES:2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC+ACID'>BES</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ntd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ntd OCA], [http://pdbe.org/5ntd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ntd RCSB], [http://www.ebi.ac.uk/pdbsum/5ntd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ntd ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested. We report here the X-ray structures of three kinetoplastid acidic LAPs (LAP-As from Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major) which were solved in the metal-free and unliganded forms, as well as in a number of ligand complexes, providing insight into ligand binding, metal ion requirements, and oligomeric state. In addition, we analyzed mutant cells defective in LAP-A in Trypanosoma brucei, strongly suggesting that the enzyme is not required for the growth of this parasite either in vitro or in vivo. In procyclic cells, LAP-A was equally distributed throughout the cytoplasm, yet upon starvation, it relocalizes in particles that concentrate in the perinuclear region. Overexpression of the enzyme conferred a growth advantage when parasites were grown in leucine-deficient medium. Overall, the results suggest that in T. brucei, LAP-A may participate in protein degradation associated with nutrient depletion. IMPORTANCE Leucine aminopeptidases (LAPs) catalyze the hydrolysis of the N-terminal amino acid of peptides and are considered potential drug targets. They are involved in multiple functions ranging from host cell invasion and provision of essential amino acids to site-specific homologous recombination and transcription regulation. In kinetoplastid parasites, there are at least three distinct LAPs. The availability of the crystal structures provides important information for drug design. Here we report the structure of the acidic LAPs from three kinetoplastids in complex with different inhibitors and explore their role in Trypanosoma brucei survival under various nutrient conditions. Importantly, the acidic LAP is dispensable for growth both in vitro and in vivo, an observation that questions its use as a specific drug target. While LAP-A is not essential, leucine depletion and subcellular localization studies performed under starvation conditions suggest a possible function of LAP-A in the response to nutrient restriction.

-	~~Authors: Timm~~, J., Wilson, K.	+	Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation in Trypanosoma brucei.,Timm J, Valente M, Garcia-Caballero D, Wilson KS, Gonzalez-Pacanowska D mSphere. 2017 Aug 16;2(4). pii: e00226-17. doi: 10.1128/mSphere.00226-17., eCollection 2017 Jul-Aug. PMID:28815215<ref>PMID:28815215</ref>

-	~~Description: Structure~~ of ~~Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5ntd" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Timm, J]]		[[Category: Timm, J]]
	[[Category: Wilson, K]]		[[Category: Wilson, K]]
		+	[[Category: Aminopeptidase]]
		+	[[Category: Hydrolase]]
		+	[[Category: M17 leucyl aminopeptidase]]
		+	[[Category: Tryanosoma brucei bestatin]]

OCA at 12:15, 17 May 2017

2017-05-17T12:15:44Z

←Older revision		Revision as of 12:15, 17 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ntd is ON HOLD	+	The entry 5ntd is ON HOLD until Paper Publication

	Authors: Timm, J., Wilson, K.		Authors: Timm, J., Wilson, K.

OCA at 09:19, 10 May 2017

2017-05-10T09:19:49Z

←Older revision		Revision as of 09:19, 10 May 2017
Line 3:		Line 3:
	The entry 5ntd is ON HOLD		The entry 5ntd is ON HOLD

-	Authors: ~~Jennifer~~ Timm, ~~Keith~~ Wilson	+	Authors: Timm, J., Wilson, K.

	Description: Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin		Description: Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Jennifer~~ Timm, ~~Keith~~ Wilson]]	+	[[Category: Timm, J]]
		+	[[Category: Wilson, K]]

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

2017-05-04T09:42:17Z

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

←Older revision

Revision as of 09:42, 4 May 2017

OCA: New page: '''Unreleased structure''' The entry 5ntd is ON HOLD Authors: Jennifer Timm, Keith Wilson Description: Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestat...

2017-05-04T09:42:16Z

New page: '''Unreleased structure''' The entry 5ntd is ON HOLD Authors: Jennifer Timm, Keith Wilson Description: Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestat...

New page

'''Unreleased structure'''

The entry 5ntd is ON HOLD

Authors: Jennifer Timm, Keith Wilson

Description: Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin
[[Category: Unreleased Structures]]
[[Category: Jennifer Timm, Keith Wilson]]