6pak - Revision history

OCA at 07:26, 11 October 2023

OCA — Wed, 11 Oct 2023 07:26:07 GMT

←Older revision		Revision as of 07:26, 11 October 2023
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	<StructureSection load='6pak' size='340' side='right'caption='[[6pak]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6pak' size='340' side='right'caption='[[6pak]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pak]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PAK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pak]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PAK 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~~>, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 1.98Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>aprE, apr, aprA, sprE, BSU10300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~224308 BACSU])</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Subtilisin Subtilisin]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62]~~ </~~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=6pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pak OCA], [https://pdbe.org/6pak PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pak RCSB], [https://www.ebi.ac.uk/pdbsum/6pak PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pak 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=6pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pak OCA], [~~http~~://pdbe.org/6pak PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pak RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pak PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pak ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SUBT_BACSU SUBT_BACSU]] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.	+	[https://www.uniprot.org/uniprot/SUBT_BACSU SUBT_BACSU] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6pak" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6pak" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Subtilisin 3D structures\|Subtilisin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Subtilisin]]~~	+	[[Category: Aihara H]]
-	[[Category: Aihara, H]]	+	[[Category: Shi K]]
-	[[Category: Shi, K]]	+	[[Category: Tang H]]
-	[[Category: Tang, H]]	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:38, 30 October 2019

OCA — Wed, 30 Oct 2019 09:38:42 GMT

←Older revision		Revision as of 09:38, 30 October 2019
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	<StructureSection load='6pak' size='340' side='right'caption='[[6pak]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6pak' size='340' side='right'caption='[[6pak]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pak]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PAK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pak]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PAK 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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aprE, apr, aprA, sprE, BSU10300 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </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=6pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pak OCA], [http://pdbe.org/6pak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pak RCSB], [http://www.ebi.ac.uk/pdbsum/6pak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pak 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=6pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pak OCA], [http://pdbe.org/6pak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pak RCSB], [http://www.ebi.ac.uk/pdbsum/6pak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pak ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/SUBT_BACSU SUBT_BACSU]] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.		[[http://www.uniprot.org/uniprot/SUBT_BACSU SUBT_BACSU]] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rational design-guided improvement of protein thermostability typically requires identification of residues or regions contributing to instability and introduction of mutations into these residues or regions. One popular method, B-FIT, utilizes B-factors to identify unstable residues or regions and combines them with other strategies, such as directed evolution. Here, we performed structure-based engineering to improve the thermostability of the subtilisin E-S7 (SES7) peptidase. The B-value of each residue was redefined in a normalized B-factor calculation, which was implemented with a refined bioinformatics analysis strategy to identify the critical area (loop 158-162) related to flexibility and to screen for suitable thermostable motif sequences in the PDB database that can act as transplant loops. In total, we analyzed 445 structures and identified 29 thermostable motifs as candidates. Using these motifs as a starting point, we performed iterative homologous modeling to obtain a desirable chimera loop and introduced five different mutations into this loop to construct thermostable SES7 proteins. Differential scanning fluorimetry (DSF) revealed increases of 7.3 degrees C in the melting temperature of an SES7 variant designated M5 compared with the wild-type. The X-ray crystallographic structure of this variant was resolved at 1.96 A resolution. The crystal structure disclosed that M5 forms more hydrogen bonds than the wild-type protein, consistent with design and molecular dynamics simulations (MDS) results. In summary, the modified B-FIT strategy reported here has yielded a subtilisin variant with improved thermostability and promising industrial applications, supporting the notion that this modified method is a powerful tool for protein engineering.
		+
		+	Enhancing subtilisin thermostability through a modified normalized B-factor analysis and loop-grafting strategy.,Tang H, Shi K, Shi C, Aihara H, Zhang J, Du G J Biol Chem. 2019 Oct 15. pii: RA119.010658. doi: 10.1074/jbc.RA119.010658. PMID:31615894<ref>PMID:31615894</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pak" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Subtilisin]]		[[Category: Subtilisin]]

OCA at 06:57, 23 October 2019

OCA — Wed, 23 Oct 2019 06:57:09 GMT

←Older revision		Revision as of 06:57, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pak is ~~ON HOLD until Paper Publication~~	+	==Insight into subtilisin E-S7 cleavage pattern based on crystal structure and hydrolysates peptide analysis==
-		+	<StructureSection load='6pak' size='340' side='right'caption='[[6pak]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pak]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PAK FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Subtilisin Subtilisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.62 3.4.21.62] </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=6pak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pak OCA], [http://pdbe.org/6pak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pak RCSB], [http://www.ebi.ac.uk/pdbsum/6pak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pak ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SUBT_BACSU SUBT_BACSU]] Subtilisin is an extracellular alkaline serine protease, it catalyzes the hydrolysis of proteins and peptide amides.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Subtilisin]]
		+	[[Category: Aihara, H]]
		+	[[Category: Shi, K]]
		+	[[Category: Tang, H]]
		+	[[Category: Hydrolase]]

OCA at 07:10, 2 October 2019

OCA — Wed, 02 Oct 2019 07:10:47 GMT

←Older revision		Revision as of 07:10, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6pak is ON HOLD	+	The entry 6pak is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6pak" [edit=sysop:move=sysop]

OCA — Wed, 19 Jun 2019 04:23:40 GMT

Protected "6pak" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:23, 19 June 2019

OCA: New page: '''Unreleased structure''' The entry 6pak is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Jun 2019 04:23:38 GMT

New page: '''Unreleased structure''' The entry 6pak is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pak is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]