OCA at 10:35, 22 November 2023

2023-11-22T10:35:19Z

←Older revision		Revision as of 10:35, 22 November 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kka is ~~ON HOLD~~	+	==Xylanase J mutant from Bacillus sp. 41M-1==
		+	<StructureSection load='6kka' size='340' side='right'caption='[[6kka]], [[Resolution\|resolution]] 2.36Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kka]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._41M-1 Bacillus sp. 41M-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KKA 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]] 2.36Å</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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6kka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kka OCA], [https://pdbe.org/6kka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kka RCSB], [https://www.ebi.ac.uk/pdbsum/6kka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kka ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9RC94_9BACI Q9RC94_9BACI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GH11 xylanase XynJ from Bacillus sp. strain 41M-1 has a beta-jellyroll fold composed of eight beta strands with a deep active-site cleft. We hypothesized that the thermostability of XynJ will increase if the flexibility of the beta strands in the jellyroll structure is decreased without impairing activity. To verify this hypothesis, we introduced random mutations into Tyr13-Arg104 and Gly169-Tyr194, both of which are located in the beta-jellyroll fold of XynJ, to construct a site saturation mutagenesis library. By screening 576 clones followed by site saturation mutation analysis of Thr82, T82A was selected as the most thermostable variant. In the hydrolysis of beechwood xylan at pH 7.8, the temperatures required to reduce initial activity by 50% in 15â¯min were 61â¯ degrees C for the wild-type XynJ (WT) and 65â¯ degrees C for T82A. The optimum hydrolysis temperatures were 60â¯ degrees C for WT and 65â¯ degrees C for T82A. There was little difference in the k(cat) and K(m) values and the pH dependence of activity between WT and T82A. Crystallographic analysis of WT and T82A revealed that thermostabilization by the T82A mutation might result from the removal of unfavorable van der Waals interactions. Thus, a highly thermostable XynJ variant was generated without impairing activity using this mutation strategy.

-	~~Authors: Suzuki, M~~., Takita, T., Nakatani, K.	+	Increase in the thermostability of GH11 xylanase XynJ from Bacillus sp. strain 41M-1 using site saturation mutagenesis.,Takita T, Nakatani K, Katano Y, Suzuki M, Kojima K, Saka N, Mikami B, Yatsunami R, Nakamura S, Yasukawa K Enzyme Microb Technol. 2019 Nov;130:109363. doi: 10.1016/j.enzmictec.2019.109363. , Epub 2019 Jun 18. PMID:31421720<ref>PMID:31421720</ref>

-	~~Description~~: ~~Xylanase J mutant from~~ Bacillus sp. 41M-1	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Nakatani, K]]	+	<div class="pdbe-citations 6kka" style="background-color:#fffaf0;"></div>
-	[[Category: Suzuki, M]]	+	== References ==
-	[[Category: Takita, T]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bacillus sp. 41M-1]]
		+	[[Category: Large Structures]]
		+	[[Category: Nakatani K]]
		+	[[Category: Suzuki M]]
		+	[[Category: Takita T]]

OCA at 04:06, 7 August 2019

2019-08-07T04:06:59Z

←Older revision		Revision as of 04:06, 7 August 2019
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	Authors: Suzuki, M., Takita, T., Nakatani, K.		Authors: Suzuki, M., Takita, T., Nakatani, K.

-	Description: ~~xylanase~~ J mutant from Bacillus sp. 41M-1	+	Description: Xylanase J mutant from Bacillus sp. 41M-1
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Nakatani, K]]		[[Category: Nakatani, K]]
	[[Category: Suzuki, M]]		[[Category: Suzuki, M]]
	[[Category: Takita, T]]		[[Category: Takita, T]]

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

2019-07-31T04:39:03Z

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

←Older revision

Revision as of 04:39, 31 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kka is ON HOLD Authors: Suzuki, M., Takita, T., Nakatani, K. Description: xylanase J mutant from Bacillus sp. 41M-1 [[Category: Unreleased Structu...

2019-07-31T04:39:02Z

New page: '''Unreleased structure''' The entry 6kka is ON HOLD Authors: Suzuki, M., Takita, T., Nakatani, K. Description: xylanase J mutant from Bacillus sp. 41M-1 [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 6kka is ON HOLD

Authors: Suzuki, M., Takita, T., Nakatani, K.

Description: xylanase J mutant from Bacillus sp. 41M-1
[[Category: Unreleased Structures]]
[[Category: Nakatani, K]]
[[Category: Suzuki, M]]
[[Category: Takita, T]]

6kka - Revision history

OCA at 10:35, 22 November 2023

OCA at 04:06, 7 August 2019

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

OCA: New page: '''Unreleased structure''' The entry 6kka is ON HOLD Authors: Suzuki, M., Takita, T., Nakatani, K. Description: xylanase J mutant from Bacillus sp. 41M-1 [[Category: Unreleased Structu...