7v9p - Revision history

OCA at 17:22, 29 November 2023

OCA — Wed, 29 Nov 2023 17:22:18 GMT

←Older revision		Revision as of 17:22, 29 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharopolyspora_erythraea_NRRL_2338 Saccharopolyspora erythraea NRRL 2338]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>		<table><tr><td colspan='2'>[[7v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharopolyspora_erythraea_NRRL_2338 Saccharopolyspora erythraea NRRL 2338]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p 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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A4F9D7_SACEN A4F9D7_SACEN]]	+	[https://www.uniprot.org/uniprot/A4F9D7_SACEN A4F9D7_SACEN]

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

OCA at 07:24, 8 September 2022

OCA — Thu, 08 Sep 2022 07:24:16 GMT

←Older revision		Revision as of 07:24, 8 September 2022
Line 1:		Line 1:

	==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==		==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==
-	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]]' scene=''>	+	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]], [[Resolution\|resolution]] 1.80Å' 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=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v9p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharopolyspora_erythraea_NRRL_2338 Saccharopolyspora erythraea NRRL 2338]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>
-	</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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p 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=ZN:ZINC+ION'>ZN</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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A4F9D7_SACEN A4F9D7_SACEN]]
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Saccharopolyspora erythraea NRRL 2338]]
	[[Category: Bao R]]		[[Category: Bao R]]
	[[Category: Zhao C]]		[[Category: Zhao C]]
	[[Category: Zhao NL]]		[[Category: Zhao NL]]

OCA at 14:38, 31 August 2022

OCA — Wed, 31 Aug 2022 14:38:59 GMT

←Older revision		Revision as of 14:38, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==		==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==
-	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>	+	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7v9p]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~	+	</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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanPM1 enzymes, a subgroup of M1 zinc-metallopeptidases, have been recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanPM1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states, and identified a unique interdomain Ca(2+) binding site as a regulatory element that modulates its domain dynamics and proteolytic activity. Inspired by this regulatory Ca(2+) binding, we developed a strategy to engineer LanPM1 enzymes for enhanced catalytic activities by strengthening interdomain associations and driving the conformational equilibrium toward their closed forms.
-
-	Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases.,Zhao C, Sheng W, Wang Y, Zheng J, Xie X, Liang Y, Wei W, Bao R, Wang H Nat Chem Biol. 2022 May 5. pii: 10.1038/s41589-022-01018-2. doi:, 10.1038/s41589-022-01018-2. PMID:35513512<ref>PMID:35513512</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7v9p" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Membrane alanyl aminopeptidase]]~~	+	[[Category: Bao R]]
-	[[Category: Bao, R]]	+	[[Category: Zhao C]]
-	[[Category: Zhao, C]]	+	[[Category: Zhao NL]]
-	[[Category: Zhao~~, N L]]~~	+
-	~~[[Category: Alanine aminopeptidase]]~~	+
-	~~[[Category: Aminopeptidase]]~~	+
-	~~[[Category: Cytosolic protein]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 08:18, 25 May 2022

OCA — Wed, 25 May 2022 08:18:19 GMT

←Older revision		Revision as of 08:18, 25 May 2022
Line 1:		Line 1:

	==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==		==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==
-	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]]' scene=''>	+	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]], [[Resolution\|resolution]] 1.80Å' 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=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7v9p]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>
-	</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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p 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=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Membrane_alanyl_aminopeptidase Membrane alanyl aminopeptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.2 3.4.11.2] </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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lanthipeptides are an important group of natural products with diverse biological functions, and their biosynthesis requires the removal of N-terminal leader peptides (LPs) by designated proteases. LanPM1 enzymes, a subgroup of M1 zinc-metallopeptidases, have been recently identified as bifunctional proteases with both endo- and aminopeptidase activities to remove LPs of class III and class IV lanthipeptides. Herein, we report the biochemical and structural characterization of EryP as the LanPM1 enzyme from the biosynthesis of class III lanthipeptide erythreapeptin. We determined X-ray crystal structures of EryP in three conformational states, the open, intermediate and closed states, and identified a unique interdomain Ca(2+) binding site as a regulatory element that modulates its domain dynamics and proteolytic activity. Inspired by this regulatory Ca(2+) binding, we developed a strategy to engineer LanPM1 enzymes for enhanced catalytic activities by strengthening interdomain associations and driving the conformational equilibrium toward their closed forms.
		+
		+	Conformational remodeling enhances activity of lanthipeptide zinc-metallopeptidases.,Zhao C, Sheng W, Wang Y, Zheng J, Xie X, Liang Y, Wei W, Bao R, Wang H Nat Chem Biol. 2022 May 5. pii: 10.1038/s41589-022-01018-2. doi:, 10.1038/s41589-022-01018-2. PMID:35513512<ref>PMID:35513512</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7v9p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bao R]]	+	[[Category: Membrane alanyl aminopeptidase]]
-	[[Category: Zhao C]]	+	[[Category: Bao, R]]
-	[[Category: Zhao NL]]	+	[[Category: Zhao, C]]
		+	[[Category: Zhao, N L]]
		+	[[Category: Alanine aminopeptidase]]
		+	[[Category: Aminopeptidase]]
		+	[[Category: Cytosolic protein]]
		+	[[Category: Hydrolase]]

OCA at 06:21, 12 May 2022

OCA — Thu, 12 May 2022 06:21:26 GMT

←Older revision		Revision as of 06:21, 12 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7v9p ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of the lanthipeptide zinc-metallopeptidase EryP from saccharopolyspora erythraea in intermediate state==
-		+	<StructureSection load='7v9p' size='340' side='right'caption='[[7v9p]]' scene=''>
-	~~Authors~~: ~~Zhao~~, C., ~~Zhao~~, N.L., ~~Bao~~, R.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7V9P FirstGlance]. <br>
-	~~Description: The crystal structure of EryP in intermediate state~~	+	</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=7v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7v9p OCA], [https://pdbe.org/7v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7v9p RCSB], [https://www.ebi.ac.uk/pdbsum/7v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7v9p ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Zhao, N.L~~]]	+	__TOC__
-	[[Category: ~~Bao, R~~]]	+	</StructureSection>
-	[[Category: Zhao~~, C~~]]	+	[[Category: Large Structures]]
		+	[[Category: Bao R]]
		+	[[Category: Zhao C]]
		+	[[Category: Zhao NL]]

OCA at 07:52, 29 September 2021

OCA — Wed, 29 Sep 2021 07:52:18 GMT

←Older revision		Revision as of 07:52, 29 September 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7v9p is ON HOLD	+	The entry 7v9p is ON HOLD until Paper Publication

	Authors: Zhao, C., Zhao, N.L., Bao, R.		Authors: Zhao, C., Zhao, N.L., Bao, R.
Line 7:		Line 7:
	Description: The crystal structure of EryP in intermediate state		Description: The crystal structure of EryP in intermediate state
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Zhao, C]]
	[[Category: Zhao, N.L]]		[[Category: Zhao, N.L]]
	[[Category: Bao, R]]		[[Category: Bao, R]]
		+	[[Category: Zhao, C]]

OCA: Protected "7v9p" [edit=sysop:move=sysop]

OCA — Wed, 08 Sep 2021 08:00:23 GMT

Protected "7v9p" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:00, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7v9p is ON HOLD Authors: Zhao, C., Zhao, N.L., Bao, R. Description: The crystal structure of EryP in intermediate state [[Category: Unreleased Stru...

OCA — Wed, 08 Sep 2021 08:00:22 GMT

New page: '''Unreleased structure''' The entry 7v9p is ON HOLD Authors: Zhao, C., Zhao, N.L., Bao, R. Description: The crystal structure of EryP in intermediate state [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 7v9p is ON HOLD

Authors: Zhao, C., Zhao, N.L., Bao, R.

Description: The crystal structure of EryP in intermediate state
[[Category: Unreleased Structures]]
[[Category: Zhao, C]]
[[Category: Zhao, N.L]]
[[Category: Bao, R]]