5zjk - Revision history

OCA at 10:28, 27 March 2024

OCA — Wed, 27 Mar 2024 10:28:01 GMT

←Older revision		Revision as of 10:28, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Myroides_sp.~~_cslb8~~ Myroides sp. ~~cslb8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Myroides_sp._CSLB8 Myroides sp. CSLB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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]] 2.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [https://pdbe.org/5zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [https://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk 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=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [https://pdbe.org/5zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [https://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A0P0DZ84_9FLAO A0A0P0DZ84_9FLAO]
-	Myroilysin is a novel bacterial member of M12A metalloproteases family with an uncommon "cysteine switch" activation mechanism and a unique "cap" structure. However, activation of pro-myroilysin is elusive. Here, mature myroilysin was obtained for structure determination by treating pro-myroilysin with trypsin. The structure of mature myroilysin showed that the active-site zinc ion of the mature protein is coordinated by three histidine residues, a water molecule, and a tyrosine residue (Tyr208) in the conserved Met-turn motif (SIMHY). The "cap" structure moves away from the active-site to leave the active cleft open; the newly formed N-terminus is deeply buried in myroilysin, and Glu151 forms a salt bridge directly with the first amino acid residue (Gly38), whereas they are far from each other in the pro-myroilysin. The mutation of Tyr208 indicates that Tyr208 plays an important role in activity of myroilysin. The proteolytic activity and thermostability of mutant E151A decreased dramatically, implying that Glu151 is not only important for catalysis, but also crucial for structural stability in myroilysin. Structural comparison also reveals differences existed between myroilysin and astacin. Our biochemical and structural data provide new insights into the activation of myroilysin and functional involvement of crucial residues Tyr208 and Glu151.	+
-		+
-	~~Crystal structure of mature myroilysin and implication for its activation mechanism.,Ran T, Li W, Sun B, Xu M, Qiu S, Xu DQ, He J, Wang W Int J Biol Macromol. 2019 Nov 28. pii~~: ~~S0141-8130(19)36556-0. doi:, 10.1016~~/~~j.ijbiomac.2019.11.205. PMID:31785296<ref>PMID:31785296<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5zjk" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Myroides sp. ~~cslb8~~]]	+	[[Category: Myroides sp. CSLB8]]
-	[[Category: Li~~, W D~~]]	+	[[Category: Li WD]]
-	[[Category: Ran~~, T T~~]]	+	[[Category: Ran TT]]
-	[[Category: Wang~~, W W~~]]	+	[[Category: Wang WW]]
-	[[Category: Xu~~, D Q]]~~	+	[[Category: Xu DQ]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 15:23, 8 June 2021

OCA — Tue, 08 Jun 2021 15:23:45 GMT

←Older revision		Revision as of 15:23, 8 June 2021
Line 3:		Line 3:
	<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Myroides_sp._cslb8 Myroides sp. cslb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Myroides_sp._cslb8 Myroides sp. cslb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [~~http~~://pdbe.org/5zjk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk 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=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [https://pdbe.org/5zjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [https://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:31, 3 June 2020

OCA — Wed, 03 Jun 2020 06:31:18 GMT

←Older revision		Revision as of 06:31, 3 June 2020
Line 3:		Line 3:
	<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure with sequence from [http://en.wikipedia.org/wiki/Myroides_sp._cslb8 Myroides sp. cslb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [http://pdbe.org/5zjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [http://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [http://pdbe.org/5zjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [http://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Myroilysin is a novel bacterial member of M12A metalloproteases family with an uncommon "cysteine switch" activation mechanism and a unique "cap" structure. However, activation of pro-myroilysin is elusive. Here, mature myroilysin was obtained for structure determination by treating pro-myroilysin with trypsin. The structure of mature myroilysin showed that the active-site zinc ion of the mature protein is coordinated by three histidine residues, a water molecule, and a tyrosine residue (Tyr208) in the conserved Met-turn motif (SIMHY). The "cap" structure moves away from the active-site to leave the active cleft open; the newly formed N-terminus is deeply buried in myroilysin, and Glu151 forms a salt bridge directly with the first amino acid residue (Gly38), whereas they are far from each other in the pro-myroilysin. The mutation of Tyr208 indicates that Tyr208 plays an important role in activity of myroilysin. The proteolytic activity and thermostability of mutant E151A decreased dramatically, implying that Glu151 is not only important for catalysis, but also crucial for structural stability in myroilysin. Structural comparison also reveals differences existed between myroilysin and astacin. Our biochemical and structural data provide new insights into the activation of myroilysin and functional involvement of crucial residues Tyr208 and Glu151.
		+
		+	Crystal structure of mature myroilysin and implication for its activation mechanism.,Ran T, Li W, Sun B, Xu M, Qiu S, Xu DQ, He J, Wang W Int J Biol Macromol. 2019 Nov 28. pii: S0141-8130(19)36556-0. doi:, 10.1016/j.ijbiomac.2019.11.205. PMID:31785296<ref>PMID:31785296</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zjk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myroides sp. cslb8]]
	[[Category: Li, W D]]		[[Category: Li, W D]]
	[[Category: Ran, T T]]		[[Category: Ran, T T]]

OCA at 07:41, 20 March 2019

OCA — Wed, 20 Mar 2019 07:41:58 GMT

←Older revision		Revision as of 07:41, 20 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zjk is ~~ON HOLD until Paper Publication~~	+	==Structure of myroilysin==
-		+	<StructureSection load='5zjk' size='340' side='right'caption='[[5zjk]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors~~: Li, W.D., ~~Ran~~, T.T., ~~Xu, D~~.Q., ~~Wang, W~~.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zjk]] is a 18 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZJK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZJK FirstGlance]. <br>
-	~~Description: Structure of myroilysin~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=5zjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zjk OCA], [http://pdbe.org/5zjk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zjk RCSB], [http://www.ebi.ac.uk/pdbsum/5zjk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zjk ProSAT]</span></td></tr>
-	[[Category: ~~Wang~~, W.W]]	+	</table>
-	[[Category: Li, ~~W.D~~]]	+	__TOC__
-	[[Category: ~~Ran~~, ~~T.T~~]]	+	</StructureSection>
-	[[Category: Xu, D.Q]]	+	[[Category: Large Structures]]
		+	[[Category: Li, W D]]
		+	[[Category: Ran, T T]]
		+	[[Category: Wang, W W]]
		+	[[Category: Xu, D Q]]
		+	[[Category: Hydrolase]]

OCA at 05:46, 23 May 2018

OCA — Wed, 23 May 2018 05:46:44 GMT

←Older revision		Revision as of 05:46, 23 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W.		Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W.
Line 7:		Line 7:
	Description: Structure of myroilysin		Description: Structure of myroilysin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xu, D.Q]]
	[[Category: Wang, W.W]]		[[Category: Wang, W.W]]
	[[Category: Li, W.D]]		[[Category: Li, W.D]]
	[[Category: Ran, T.T]]		[[Category: Ran, T.T]]
		+	[[Category: Xu, D.Q]]

OCA at 04:30, 4 April 2018

OCA — Wed, 04 Apr 2018 04:30:48 GMT

←Older revision		Revision as of 04:30, 4 April 2018
Line 5:		Line 5:
	Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W.		Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W.

-	Description: myroilysin	+	Description: Structure of myroilysin
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Xu, D.Q]]		[[Category: Xu, D.Q]]

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

OCA — Wed, 28 Mar 2018 05:12:08 GMT

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

←Older revision

Revision as of 05:12, 28 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zjk is ON HOLD Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W. Description: myroilysin Category: Unreleased Structures [[Category: Xu, D.Q]...

OCA — Wed, 28 Mar 2018 05:12:07 GMT

New page: '''Unreleased structure''' The entry 5zjk is ON HOLD Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W. Description: myroilysin Category: Unreleased Structures [[Category: Xu, D.Q]...

New page

'''Unreleased structure'''

The entry 5zjk is ON HOLD

Authors: Li, W.D., Ran, T.T., Xu, D.Q., Wang, W.W.

Description: myroilysin
[[Category: Unreleased Structures]]
[[Category: Xu, D.Q]]
[[Category: Wang, W.W]]
[[Category: Li, W.D]]
[[Category: Ran, T.T]]