7neb - Revision history

OCA at 12:33, 1 February 2024

2024-02-01T12:33:46Z

←Older revision		Revision as of 12:33, 1 February 2024
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	<StructureSection load='7neb' size='340' side='right'caption='[[7neb]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='7neb' size='340' side='right'caption='[[7neb]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7neb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet1 Thet1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7neb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobaculum_terrenum_ATCC_BAA-798 Thermobaculum terrenum ATCC BAA-798]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NA:SODIUM+ION'>NA</scene>~~, ~~<scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[7nea\|7nea]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ilvE, Tter_1720 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~525904 THET1])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Branched~~-~~chain~~-~~amino-acid_transaminase Branched-chain-amino-acid transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.42 2.6.1.42]~~ </~~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=7neb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neb OCA], [https://pdbe.org/7neb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neb RCSB], [https://www.ebi.ac.uk/pdbsum/7neb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neb 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=7neb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neb OCA], [https://pdbe.org/7neb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neb RCSB], [https://www.ebi.ac.uk/pdbsum/7neb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/D1CCW1_THET1 D1CCW1_THET1]] Acts on leucine, isoleucine and valine.[RuleBase:RU364094]	+	[https://www.uniprot.org/uniprot/D1CCW1_THET1 D1CCW1_THET1] Acts on leucine, isoleucine and valine.[RuleBase:RU364094]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Branched-chain-amino-acid transaminase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet1~~]]	+	[[Category: Thermobaculum terrenum ATCC BAA-798]]
-	[[Category: Bezsudnova~~, E Y~~]]	+	[[Category: Bezsudnova EY]]
-	[[Category: Boyko~~, K M~~]]	+	[[Category: Boyko KM]]
-	[[Category: Nikolaeva~~, A Y~~]]	+	[[Category: Nikolaeva AY]]
-	[[Category: Petrova, T]]	+	[[Category: Petrova T]]
-	[[Category: Popov~~, V O~~]]	+	[[Category: Popov VO]]
-	[[Category: Rakitina~~, T V~~]]	+	[[Category: Rakitina TV]]
-	[[Category: Suplatov~~, D A~~]]	+	[[Category: Suplatov DA]]
-	[[Category: Zeifman~~, Y S]]~~	+	[[Category: Zeifman YS]]
-	~~[[Category: Aminotransferase]]~~	+
-	~~[[Category: Bcat]]~~	+
-	~~[[Category: Branched-chain amino acid aminotransferase]]~~	+
-	~~[[Category: Iv-fold type]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Plp-dependent enzyme]]~~	+
-	~~[[Category: Transaminase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:39, 19 January 2022

2022-01-19T07:39:09Z

←Older revision		Revision as of 07:39, 19 January 2022
Line 1:		Line 1:

	==Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)==		==Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)==
-	<StructureSection load='7neb' size='340' side='right'caption='[[7neb]]' scene=''>	+	<StructureSection load='7neb' size='340' side='right'caption='[[7neb]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7neb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet1 Thet1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEB FirstGlance]. <br>
-	</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=7neb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neb OCA], [https://pdbe.org/7neb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neb RCSB], [https://www.ebi.ac.uk/pdbsum/7neb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neb ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7nea\|7nea]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ilvE, Tter_1720 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=525904 THET1])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Branched-chain-amino-acid_transaminase Branched-chain-amino-acid transaminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.6.1.42 2.6.1.42] </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=7neb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neb OCA], [https://pdbe.org/7neb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neb RCSB], [https://www.ebi.ac.uk/pdbsum/7neb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/D1CCW1_THET1 D1CCW1_THET1]] Acts on leucine, isoleucine and valine.[RuleBase:RU364094]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Creating biocatalysts for (R)-selective amination effectively is highly desirable in organic synthesis. Despite noticeable progress in the engineering of (R)-amine activity in pyridoxal-5'-phosphate-dependent transaminases of fold type IV, the specialization of the activity is still an intuitive task, as there is poor understanding of sequence-structure-function relationships. In this study, we analyzed this relationship in transaminase from Thermobaculum terrenum, distinguished by expanded substrate specificity and activity in reactions with L-amino acids and (R)-(+)-1-phenylethylamine using alpha-ketoglutarate and pyruvate as amino acceptors. We performed site-directed mutagenesis to create a panel of the enzyme variants, which differ in the active site residues from the parent enzyme to a putative transaminase specific to (R)-primary amines. The variants were examined in the overall transamination reactions and half-reaction with (R)-(+)-1-phenylethylamine. A structural analysis of the most prominent variants revealed a spatial reorganization in the active sites, which caused changes in activity. Although the specialization to (R)-amine transaminase was not implemented, we succeeded in understanding the role of the particular active site residues in expanding substrate specificity of the enzyme. We showed that the specificity for (R)-(+)-1-phenylethylamine in transaminase from T. terrenum arises without sacrificing the specificity for L-amino acids and alpha-ketoglutarate and in consensus with it.
		+
		+	Probing the role of the residues in the active site of the transaminase from Thermobaculum terrenum.,Bezsudnova EY, Nikolaeva AY, Bakunova AK, Rakitina TV, Suplatov DA, Popov VO, Boyko KM PLoS One. 2021 Jul 29;16(7):e0255098. doi: 10.1371/journal.pone.0255098., eCollection 2021. PMID:34324538<ref>PMID:34324538</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7neb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Branched-chain-amino-acid transaminase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bezsudnova EY]]	+	[[Category: Thet1]]
-	[[Category: Boyko KM]]	+	[[Category: Bezsudnova, E Y]]
-	[[Category: Nikolaeva AY]]	+	[[Category: Boyko, K M]]
-	[[Category: Petrova T]]	+	[[Category: Nikolaeva, A Y]]
-	[[Category: Popov VO]]	+	[[Category: Petrova, T]]
-	[[Category: Rakitina TV]]	+	[[Category: Popov, V O]]
-	[[Category: Suplatov DA]]	+	[[Category: Rakitina, T V]]
-	[[Category: Zeifman YS]]	+	[[Category: Suplatov, D A]]
		+	[[Category: Zeifman, Y S]]
		+	[[Category: Aminotransferase]]
		+	[[Category: Bcat]]
		+	[[Category: Branched-chain amino acid aminotransferase]]
		+	[[Category: Iv-fold type]]
		+	[[Category: Mutant]]
		+	[[Category: Plp-dependent enzyme]]
		+	[[Category: Transaminase]]
		+	[[Category: Transferase]]

OCA at 09:58, 7 July 2021

2021-07-07T09:58:26Z

←Older revision		Revision as of 09:58, 7 July 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7neb ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)==
-		+	<StructureSection load='7neb' size='340' side='right'caption='[[7neb]]' scene=''>
-	~~Authors~~: ~~Boyko, K~~.M.~~, Petrova, T~~.~~, Nikolaeva, A~~.Y.~~, Zeifman, Y~~.S., ~~Rakitina, T~~.V., ~~Suplatov~~, D.A., ~~Popov, V~~.O., ~~Bezsudnova, E~~.Y.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NEB FirstGlance]. <br>
-	~~Description: Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)~~	+	</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=7neb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7neb OCA], [https://pdbe.org/7neb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7neb RCSB], [https://www.ebi.ac.uk/pdbsum/7neb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7neb ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Zeifman, Y.S~~]]	+	__TOC__
-	[[Category: Boyko~~, K.M~~]]	+	</StructureSection>
-	[[Category: ~~Popov, V.O~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nikolaeva, A.Y~~]]	+	[[Category: Bezsudnova EY]]
-	[[Category: ~~Rakitina, T.V~~]]	+	[[Category: Boyko KM]]
-	[[Category: ~~Bezsudnova, E.Y~~]]	+	[[Category: Nikolaeva AY]]
-	[[Category: ~~Petrova, T~~]]	+	[[Category: Petrova T]]
-	[[Category: ~~Suplatov, D.A~~]]	+	[[Category: Popov VO]]
		+	[[Category: Rakitina TV]]
		+	[[Category: Suplatov DA]]
		+	[[Category: Zeifman YS]]

OCA at 14:52, 10 March 2021

2021-03-10T14:52:57Z

←Older revision		Revision as of 14:52, 10 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7neb is ON HOLD	+	The entry 7neb is ON HOLD until Paper Publication

	Authors: Boyko, K.M., Petrova, T., Nikolaeva, A.Y., Zeifman, Y.S., Rakitina, T.V., Suplatov, D.A., Popov, V.O., Bezsudnova, E.Y.		Authors: Boyko, K.M., Petrova, T., Nikolaeva, A.Y., Zeifman, Y.S., Rakitina, T.V., Suplatov, D.A., Popov, V.O., Bezsudnova, E.Y.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Zeifman, Y.S]]		[[Category: Zeifman, Y.S]]
-	[[Category: Petrova, T]]
	[[Category: Boyko, K.M]]		[[Category: Boyko, K.M]]
-	[[Category: Suplatov, D.A]]
	[[Category: Popov, V.O]]		[[Category: Popov, V.O]]
	[[Category: Nikolaeva, A.Y]]		[[Category: Nikolaeva, A.Y]]
	[[Category: Rakitina, T.V]]		[[Category: Rakitina, T.V]]
	[[Category: Bezsudnova, E.Y]]		[[Category: Bezsudnova, E.Y]]
		+	[[Category: Petrova, T]]
		+	[[Category: Suplatov, D.A]]

OCA: Protected "7neb" [edit=sysop:move=sysop]

2021-02-10T09:26:53Z

Protected "7neb" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:26, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7neb is ON HOLD Authors: Boyko, K.M., Petrova, T., Nikolaeva, A.Y., Zeifman, Y.S., Rakitina, T.V., Suplatov, D.A., Popov, V.O., Bezsudnova, E.Y. De...

2021-02-10T09:26:52Z

New page: '''Unreleased structure''' The entry 7neb is ON HOLD Authors: Boyko, K.M., Petrova, T., Nikolaeva, A.Y., Zeifman, Y.S., Rakitina, T.V., Suplatov, D.A., Popov, V.O., Bezsudnova, E.Y. De...

New page

'''Unreleased structure'''

The entry 7neb is ON HOLD

Authors: Boyko, K.M., Petrova, T., Nikolaeva, A.Y., Zeifman, Y.S., Rakitina, T.V., Suplatov, D.A., Popov, V.O., Bezsudnova, E.Y.

Description: Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum (M4 mutant)
[[Category: Unreleased Structures]]
[[Category: Zeifman, Y.S]]
[[Category: Petrova, T]]
[[Category: Boyko, K.M]]
[[Category: Suplatov, D.A]]
[[Category: Popov, V.O]]
[[Category: Nikolaeva, A.Y]]
[[Category: Rakitina, T.V]]
[[Category: Bezsudnova, E.Y]]