8pzy - Revision history

OCA at 09:03, 6 December 2023

OCA — Wed, 06 Dec 2023 09:03:54 GMT

←Older revision		Revision as of 09:03, 6 December 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pzy is ~~ON HOLD until Paper~~ Publication	+	==Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 - hexameric assembly with manganese bound==
		+	<StructureSection load='8pzy' size='340' side='right'caption='[[8pzy]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pzy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PA14 Pseudomonas aeruginosa PA14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PZY FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.97Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=P03:2-[3-[3-(2-HYDROXYETHOXY)PROPOXY]PROPOXY]ETHANOL'>P03</scene></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=8pzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pzy OCA], [https://pdbe.org/8pzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pzy RCSB], [https://www.ebi.ac.uk/pdbsum/8pzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pzy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMPA_PSEAB AMPA_PSEAB] Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Intracellular leucine aminopeptidases (PepA) are metalloproteases from the family M17. These enzymes catalyze peptide bond cleavage, removing N-terminal residues from peptide and protein substrates, with consequences for protein homeostasis and quality control. While general mechanistic studies using model substrates have been conducted on PepA enzymes from various organisms, specific information about their substrate preferences and promiscuity, choice of metal, activation mechanisms, and the steps that limit steady-state turnover remain unexplored. Here, we dissected the catalytic and chemical mechanisms of PaPepA: a leucine aminopeptidase from Pseudomonas aeruginosa. Cleavage assays using peptides and small-molecule substrate mimics allowed us to propose a mechanism for catalysis. Steady-state and pre-steady-state kinetics, pH rate profiles, solvent kinetic isotope effects, and biophysical techniques were used to evaluate metal binding and activation. This revealed that metal binding to a tight affinity site is insufficient for enzyme activity; binding to a weaker affinity site is essential for catalysis. Progress curves for peptide hydrolysis and crystal structures of free and inhibitor-bound PaPepA revealed that PaPepA cleaves peptide substrates in a processive manner. We propose three distinct modes for activity regulation: tight packing of PaPepA in a hexameric assembly controls substrate length and reaction processivity; the product leucine acts as an inhibitor, and the high concentration of metal ions required for activation limits catalytic turnover. Our work uncovers catalysis by a metalloaminopeptidase, revealing the intricacies of metal activation and substrate selection. This will pave the way for a deeper understanding of metalloenzymes and processive peptidases/proteases.

-	~~Authors~~:	+	Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase.,Simpson MC, Harding CJ, Czekster RM, Remmel L, Bode BE, Czekster CM Biochemistry. 2023 Nov 4. doi: 10.1021/acs.biochem.3c00420. PMID:37924287<ref>PMID:37924287</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pzy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseudomonas aeruginosa PA14]]
		+	[[Category: Czekster CM]]
		+	[[Category: Harding CJ]]
		+	[[Category: Simpson MC]]

OCA: Replacing page with ''''Unreleased structure''' The entry 8pzy is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

OCA — Wed, 22 Nov 2023 05:39:00 GMT

Replacing page with ''''Unreleased structure''' The entry 8pzy is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures'

←Older revision		Revision as of 05:39, 22 November 2023
Line 1:		Line 1:
		+	'''Unreleased structure'''

-	~~==Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 - hexameric assembly with manganese bound==~~	+	The entry 8pzy is ON HOLD until Paper Publication
-	~~<StructureSection load='~~8pzy~~' size='340' side='right'caption='[[8pzy]], [[Resolution\|resolution]] 1.97Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[8pzy]]~~ is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PA14 Pseudomonas aeruginosa PA14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PZY FirstGlance]. <br>	+
-	~~</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.97Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=P03:2-[3-[3-(2-HYDROXYETHOXY)PROPOXY]PROPOXY]ETHANOL'>P03</scene></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=8pzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pzy OCA], [https://pdbe.org/8pzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pzy RCSB], [https://www.ebi.ac.uk/pdbsum/8pzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pzy ProSAT]</span></td></tr>	+
-	~~</table>~~	+
-	~~== Function ==~~	+
-	[https://www.uniprot.org/uniprot/AMPA_PSEAB AMPA_PSEAB] Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	== Publication ~~Abstract from PubMed ==~~	+
-	Intracellular leucine aminopeptidases (PepA) are metalloproteases from the family M17. These enzymes catalyze peptide bond cleavage, removing N-terminal residues from peptide and protein substrates, with consequences for protein homeostasis and quality control. While general mechanistic studies using model substrates have been conducted on PepA enzymes from various organisms, specific information about their substrate preferences and promiscuity, choice of metal, activation mechanisms, and the steps that limit steady-state turnover remain unexplored. Here, we dissected the catalytic and chemical mechanisms of PaPepA: a leucine aminopeptidase from Pseudomonas aeruginosa. Cleavage assays using peptides and small-molecule substrate mimics allowed us to propose a mechanism for catalysis. Steady-state and pre-steady-state kinetics, pH rate profiles, solvent kinetic isotope effects, and biophysical techniques were used to evaluate metal binding and activation. This revealed that metal binding to a tight affinity site is insufficient for enzyme activity; binding to a weaker affinity site is essential for catalysis. Progress curves for peptide hydrolysis and crystal structures of free and inhibitor-bound PaPepA revealed that PaPepA cleaves peptide substrates in a processive manner. We propose three distinct modes for activity regulation: tight packing of PaPepA in a hexameric assembly controls substrate length and reaction processivity; the product leucine acts as an inhibitor, and the high concentration of metal ions required for activation limits catalytic turnover. Our work uncovers catalysis by a metalloaminopeptidase, revealing the intricacies of metal activation and substrate selection. This will pave the way for a deeper understanding of metalloenzymes and processive peptidases/proteases.	+

-	~~Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase.,Simpson MC, Harding CJ, Czekster RM, Remmel L, Bode BE, Czekster CM Biochemistry. 2023 Nov 4. doi~~: ~~10.1021/acs.biochem.3c00420. PMID:37924287<ref>PMID:37924287</ref>~~	+	Authors:

-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	Description:
-	~~</div>~~	+	[[Category: Unreleased Structures]]
-	~~<div class="pdbe-citations 8pzy" style="background-color~~:~~#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	[[Category: ~~Large~~ Structures]]	+
-	~~[[Category: Pseudomonas aeruginosa PA14]]~~	+
-	~~[[Category: Czekster CM]]~~	+
-	~~[[Category: Harding CJ]]~~	+
-	~~[[Category: Simpson MC~~]]	+

OCA at 07:41, 15 November 2023

OCA — Wed, 15 Nov 2023 07:41:02 GMT

←Older revision		Revision as of 07:41, 15 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8pzy is ~~ON HOLD until Paper~~ Publication	+	==Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 - hexameric assembly with manganese bound==
		+	<StructureSection load='8pzy' size='340' side='right'caption='[[8pzy]], [[Resolution\|resolution]] 1.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8pzy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PA14 Pseudomonas aeruginosa PA14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PZY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PZY FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.97Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=P03:2-[3-[3-(2-HYDROXYETHOXY)PROPOXY]PROPOXY]ETHANOL'>P03</scene></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=8pzy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pzy OCA], [https://pdbe.org/8pzy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pzy RCSB], [https://www.ebi.ac.uk/pdbsum/8pzy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pzy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AMPA_PSEAB AMPA_PSEAB] Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Intracellular leucine aminopeptidases (PepA) are metalloproteases from the family M17. These enzymes catalyze peptide bond cleavage, removing N-terminal residues from peptide and protein substrates, with consequences for protein homeostasis and quality control. While general mechanistic studies using model substrates have been conducted on PepA enzymes from various organisms, specific information about their substrate preferences and promiscuity, choice of metal, activation mechanisms, and the steps that limit steady-state turnover remain unexplored. Here, we dissected the catalytic and chemical mechanisms of PaPepA: a leucine aminopeptidase from Pseudomonas aeruginosa. Cleavage assays using peptides and small-molecule substrate mimics allowed us to propose a mechanism for catalysis. Steady-state and pre-steady-state kinetics, pH rate profiles, solvent kinetic isotope effects, and biophysical techniques were used to evaluate metal binding and activation. This revealed that metal binding to a tight affinity site is insufficient for enzyme activity; binding to a weaker affinity site is essential for catalysis. Progress curves for peptide hydrolysis and crystal structures of free and inhibitor-bound PaPepA revealed that PaPepA cleaves peptide substrates in a processive manner. We propose three distinct modes for activity regulation: tight packing of PaPepA in a hexameric assembly controls substrate length and reaction processivity; the product leucine acts as an inhibitor, and the high concentration of metal ions required for activation limits catalytic turnover. Our work uncovers catalysis by a metalloaminopeptidase, revealing the intricacies of metal activation and substrate selection. This will pave the way for a deeper understanding of metalloenzymes and processive peptidases/proteases.

-	~~Authors~~:	+	Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase.,Simpson MC, Harding CJ, Czekster RM, Remmel L, Bode BE, Czekster CM Biochemistry. 2023 Nov 4. doi: 10.1021/acs.biochem.3c00420. PMID:37924287<ref>PMID:37924287</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8pzy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pseudomonas aeruginosa PA14]]
		+	[[Category: Czekster CM]]
		+	[[Category: Harding CJ]]
		+	[[Category: Simpson MC]]

OCA at 07:24, 30 August 2023

OCA — Wed, 30 Aug 2023 07:24:48 GMT

←Older revision		Revision as of 07:24, 30 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8pzy is ON HOLD	+	The entry 8pzy is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8pzy" [edit=sysop:move=sysop]

OCA — Wed, 02 Aug 2023 09:17:30 GMT

Protected "8pzy" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:17, 2 August 2023

OCA: New page: '''Unreleased structure''' The entry 8pzy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Aug 2023 09:17:29 GMT

New page: '''Unreleased structure''' The entry 8pzy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8pzy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]