OCA at 09:14, 30 August 2023

OCA — Wed, 30 Aug 2023 09:14:38 GMT

←Older revision		Revision as of 09:14, 30 August 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8onl is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A==
		+	<StructureSection load='8onl' size='340' side='right'caption='[[8onl]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8onl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aminobacterium_colombiense Aminobacterium colombiense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8ONL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ONL 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]] 1.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=8onl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8onl OCA], [https://pdbe.org/8onl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8onl RCSB], [https://www.ebi.ac.uk/pdbsum/8onl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8onl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D5EHC5_AMICL D5EHC5_AMICL]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The development of biocatalysts requires reorganization of the enzyme's active site to facilitate the productive binding of the target substrate and improve turnover number at desired conditions. Pyridoxal-5'-phosphate (PLP) - dependent transaminases are highly efficient biocatalysts for asymmetric amination of ketones and keto acids. However, transaminases, being stereoselective enzymes, have a narrow substrate specificity due to the ordered structure of the active site and work only in neutral-alkaline media. Here, we investigated the d-amino acid transaminase from Aminobacterium colombiense, with the active site organized differently from that of the canonical d-amino acid transaminase from Bacillus sp. YM-1. Using a combination of site-directed mutagenesis, kinetic analysis, molecular modeling, and structural analysis we determined the active site residues responsible for substrate binding, substrate differentiation, thermostability of a functional dimer, and affecting the pH optimum. We demonstrated that the high specificity toward d-glutamate/alpha-ketoglutarate is due to the interactions of a gamma-carboxylate group with K237 residue, while binding of other substrates stems from the effectiveness of their accommodation in the active site optimized for d-glutamate/alpha-ketoglutarate binding. Furthermore, we showed that the K237A substitution shifts the catalytic activity optimum to acidic pH. Our findings are useful for achieving target substrate specificity and demonstrate the potential for developing and optimizing transaminases for various applications.

-	~~Authors~~: Matyuta, ~~I.O.~~, ~~Boyko~~, ~~K.M.~~, Minyaev, ~~M.E.~~, ~~Shilova~~, ~~S.A.~~, Bezsudnova~~, E~~.Y.~~, Popov, V~~.O.	+	In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.,Shilova SA, Matyuta IO, Khrenova MG, Nikolaeva AY, Klyachko NL, Minyaev ME, Khomutov AR, Boyko KM, Popov VO, Bezsudnova EY Biochem J. 2023 Aug 30;480(16):1267-1284. doi: 10.1042/BCJ20230233. PMID:37548495<ref>PMID:37548495</ref>

-	~~Description: Crystal structure~~ of D-~~amino acid aminotransferase from~~ Aminobacterium colombiense ~~point mutant E113A~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Matyuta, I.O~~]]	+	<div class="pdbe-citations 8onl" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Shilova, S.A~~]]	+	== References ==
-	[[Category: ~~Boyko, K.M~~]]	+	<references/>
-	[[Category: ~~Popov, V.O~~]]	+	__TOC__
-	[[Category: ~~Bezsudnova, E.Y~~]]	+	</StructureSection>
-	[[Category: ~~Minyaev, M.E~~]]	+	[[Category: Aminobacterium colombiense]]
		+	[[Category: Large Structures]]
		+	[[Category: Bezsudnova EY]]
		+	[[Category: Boyko KM]]
		+	[[Category: Matyuta IO]]
		+	[[Category: Minyaev ME]]
		+	[[Category: Popov VO]]
		+	[[Category: Shilova SA]]

OCA: Protected "8onl" [edit=sysop:move=sysop]

OCA — Wed, 12 Apr 2023 19:00:06 GMT

Protected "8onl" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:00, 12 April 2023

OCA: New page: '''Unreleased structure''' The entry 8onl is ON HOLD until Paper Publication Authors: Matyuta, I.O., Boyko, K.M., Minyaev, M.E., Shilova, S.A., Bezsudnova, E.Y., Popov, V.O. Descriptio...

OCA — Wed, 12 Apr 2023 19:00:04 GMT

New page: '''Unreleased structure''' The entry 8onl is ON HOLD until Paper Publication Authors: Matyuta, I.O., Boyko, K.M., Minyaev, M.E., Shilova, S.A., Bezsudnova, E.Y., Popov, V.O. Descriptio...

New page

'''Unreleased structure'''

The entry 8onl is ON HOLD until Paper Publication

Authors: Matyuta, I.O., Boyko, K.M., Minyaev, M.E., Shilova, S.A., Bezsudnova, E.Y., Popov, V.O.

Description: Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A
[[Category: Unreleased Structures]]
[[Category: Matyuta, I.O]]
[[Category: Shilova, S.A]]
[[Category: Boyko, K.M]]
[[Category: Popov, V.O]]
[[Category: Bezsudnova, E.Y]]
[[Category: Minyaev, M.E]]

8onl - Revision history

OCA at 09:14, 30 August 2023

OCA: Protected "8onl" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 8onl is ON HOLD until Paper Publication Authors: Matyuta, I.O., Boyko, K.M., Minyaev, M.E., Shilova, S.A., Bezsudnova, E.Y., Popov, V.O. Descriptio...