4jp8 - Revision history

OCA at 14:25, 8 November 2023

2023-11-08T14:25:00Z

←Older revision		Revision as of 14:25, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jp8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JP8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jp8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JP8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.21Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [https://pdbe.org/4jp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [https://www.ebi.ac.uk/pdbsum/4jp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp8 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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [https://pdbe.org/4jp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [https://www.ebi.ac.uk/pdbsum/4jp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp8 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:29, 24 November 2022

2022-11-24T11:29:00Z

←Older revision		Revision as of 11:29, 24 November 2022
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	==Crystal structure of Pro-F17H/S324A==		==Crystal structure of Pro-F17H/S324A==
-	<StructureSection load='4jp8' size='340' side='right' caption='[[4jp8]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='4jp8' size='340' side='right'caption='[[4jp8]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jp8]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JP8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jp8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JP8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1675 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [https://pdbe.org/4jp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [https://www.ebi.ac.uk/pdbsum/4jp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp8 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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [~~http~~://pdbe.org/4jp8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jp8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp8 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.	+	[https://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4jp8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4jp8" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Subtilisin 3D structures\|Subtilisin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Kanaya, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Koga, Y~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
-	[[Category: ~~Uehara, R~~]]	+	[[Category: Kanaya S]]
-	[[Category: ~~You, D J~~]]	+	[[Category: Koga Y]]
-	[[Category: ~~Yuzaki, K~~]]	+	[[Category: Uehara R]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: You DJ]]
-	[[Category: ~~Subtilisin-like serine protease]]~~	+	[[Category: Yuzaki K]]
-	~~[[Category: Subtillisin]]~~	+
-	~~[[Category: Thermococcus kodakarensis~~]]	+

OCA at 09:13, 15 November 2017

2017-11-15T09:13:13Z

←Older revision		Revision as of 09:13, 15 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4jp8" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4jp8" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Subtilisin\|Subtilisin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:56, 4 August 2016

2016-08-04T12:56:01Z

←Older revision		Revision as of 12:56, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Pro-F17H/S324A==		==Crystal structure of Pro-F17H/S324A==
	<StructureSection load='4jp8' size='340' side='right' caption='[[4jp8]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='4jp8' size='340' side='right' caption='[[4jp8]], [[Resolution\|resolution]] 2.21Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1675 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1675 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [http://www.ebi.ac.uk/pdbsum/4jp8 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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [http://pdbe.org/4jp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [http://www.ebi.ac.uk/pdbsum/4jp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jp8 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 4jp8" style="background-color:#fffaf0;"></div>

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

OCA at 14:46, 24 December 2014

2014-12-24T14:46:03Z

←Older revision		Revision as of 14:46, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jp8\| PDB~~=4jp8 \| ~~SCENE~~= }}	+	==Crystal structure of Pro-F17H/S324A==
-	===~~Crystal~~ structure ~~of Pro~~-~~F17H~~/~~S324A~~===	+	<StructureSection load='4jp8' size='340' side='right' caption='[[4jp8]], [[Resolution\|resolution]] 2.21Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24115021}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4jp8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JP8 FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1675 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</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=4jp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jp8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jp8 RCSB], [http://www.ebi.ac.uk/pdbsum/4jp8 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.		[[http://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tk-subtilisin (Gly70-Gly398) is a subtilisin homolog from Thermococcus kodakarensis. Active Tk-subtilisin is produced from its inactive precursor, Pro-Tk-subtilisin (Gly1-Gly398), by autoprocessing and degradation of the propeptide (Tk-propeptide, Gly1-Leu69). This activation process is extremely slow at moderate temperatures owing to high stability of Tk-propeptide. Tk-propeptide is stabilized by the hydrophobic core. To examine whether a single nonpolar-to-polar amino acid substitution at this core affects the activation rate of Pro-Tk-subtilisin, the Pro-Tk-subtilisin derivative with the Phe17 --> His mutation (Pro-F17H), Tk-propeptide derivative with the same mutation (F17H-propeptide), and two active-site mutants of Pro-F17H (Pro-F17H/S324A and Pro-F17H/S324C) were constructed. The crystal structure of Pro-F17H/S324A was nearly identical to that of Pro-S324A, indicating that the mutation does not affect the structure of Pro-Tk-subtilisin. The refolding rate of Pro-F17H/S324A and autoprocessing rate of Pro-F17H/S324C were also nearly identical to those of their parent proteins (Pro-S324A and Pro-S324C). However, the activation rate of Pro-F17H greatly increased when compared with that of Pro-Tk-subtilisin, such that Pro-F17H is efficiently activated even at 40 degrees C. The far-UV circular dichroism spectrum of F17H-propeptide did not exhibit a broad trough at 205-230 nm, which is observed in the spectrum of Tk-propeptide. F17H-propeptide is more susceptible to chymotryptic degradation than Tk-propeptide. These results suggest that F17H-propeptide is unfolded in an isolated form and is therefore rapidly degraded by Tk-subtilisin. Thus, destabilization of the hydrophobic core of Tk-propeptide by a nonpolar-to-polar amino acid substitution is an effective way to increase the activation rate of Pro-Tk-subtilisin.
		+
		+	Increase in activation rate of Pro-Tk-subtilisin by a single nonpolar-to-polar amino acid substitution at the hydrophobic core of the propeptide domain.,Yuzaki K, Sanda Y, You DJ, Uehara R, Koga Y, Kanaya S Protein Sci. 2013 Dec;22(12):1711-21. doi: 10.1002/pro.2371. Epub 2013 Oct 19. PMID:24115021<ref>PMID:24115021</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4jp8]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=4JP8 OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:024115021</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Subtilisin\|Subtilisin]]
-	[[Category: Kanaya, S.]]	+	== References ==
-	[[Category: Koga, Y.]]	+	<references/>
-	[[Category: Uehara, R.]]	+	__TOC__
-	[[Category: You, D J.]]	+	</StructureSection>
-	[[Category: Yuzaki, K.]]	+	[[Category: Kanaya, S]]
		+	[[Category: Koga, Y]]
		+	[[Category: Uehara, R]]
		+	[[Category: You, D J]]
		+	[[Category: Yuzaki, K]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Subtilisin-like serine protease]]		[[Category: Subtilisin-like serine protease]]
	[[Category: Subtillisin]]		[[Category: Subtillisin]]
	[[Category: Thermococcus kodakarensis]]		[[Category: Thermococcus kodakarensis]]

OCA at 07:40, 29 January 2014

2014-01-29T07:40:27Z

←Older revision		Revision as of 07:40, 29 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4jp8\| PDB=4jp8 \| SCENE= }}
		+	===Crystal structure of Pro-F17H/S324A===
		+	{{ABSTRACT_PUBMED_24115021}}

-	~~The entry 4jp8 is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/TKSU_THEKO TKSU_THEKO]] Has a broad substrate specificity with a slight preference to large hydrophobic amino acid residues at the P1 position.

-	~~Authors~~: ~~Yuzaki, K., You, D.J~~.~~, Uehara, R~~.~~, Koga, Y~~.~~, Kanaya, S~~.	+	==About this Structure==
		+	[[4jp8]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JP8 OCA].

-	~~Description~~: ~~Crystal structure of Pro-F17H~~/~~S324A~~	+	==Reference==
		+	<ref group="xtra">PMID:024115021</ref><references group="xtra"/><references/>
		+	[[Category: Kanaya, S.]]
		+	[[Category: Koga, Y.]]
		+	[[Category: Uehara, R.]]
		+	[[Category: You, D J.]]
		+	[[Category: Yuzaki, K.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Subtilisin-like serine protease]]
		+	[[Category: Subtillisin]]
		+	[[Category: Thermococcus kodakarensis]]

OCA at 13:02, 3 July 2013

2013-07-03T13:02:42Z

←Older revision		Revision as of 13:02, 3 July 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jp8 is ON HOLD	+	The entry 4jp8 is ON HOLD until Paper Publication

	Authors: Yuzaki, K., You, D.J., Uehara, R., Koga, Y., Kanaya, S.		Authors: Yuzaki, K., You, D.J., Uehara, R., Koga, Y., Kanaya, S.

	Description: Crystal structure of Pro-F17H/S324A		Description: Crystal structure of Pro-F17H/S324A

OCA: Protected "4jp8" [edit=sysop:move=sysop]

2013-03-27T08:21:26Z

Protected "4jp8" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:21, 27 March 2013

OCA: New page: '''Unreleased structure''' The entry 4jp8 is ON HOLD Authors: Yuzaki, K., You, D.J., Uehara, R., Koga, Y., Kanaya, S. Description: Crystal structure of Pro-F17H/S324A

2013-03-27T08:21:25Z

New page: '''Unreleased structure''' The entry 4jp8 is ON HOLD Authors: Yuzaki, K., You, D.J., Uehara, R., Koga, Y., Kanaya, S. Description: Crystal structure of Pro-F17H/S324A

New page

'''Unreleased structure'''

The entry 4jp8 is ON HOLD

Authors: Yuzaki, K., You, D.J., Uehara, R., Koga, Y., Kanaya, S.

Description: Crystal structure of Pro-F17H/S324A