7lk1 - Revision history

OCA at 14:58, 13 March 2024

OCA — Wed, 13 Mar 2024 14:58:33 GMT

←Older revision		Revision as of 14:58, 13 March 2024
Line 12:		Line 12:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/OAT_HUMAN OAT_HUMAN]		[https://www.uniprot.org/uniprot/OAT_HUMAN OAT_HUMAN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The inhibition of human ornithine delta-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
-
-	Turnover and Inactivation Mechanisms for (S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase.,Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB J Am Chem Soc. 2021 Jun 16;143(23):8689-8703. doi: 10.1021/jacs.1c02456. Epub, 2021 Jun 7. PMID:34097381<ref>PMID:34097381</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7lk1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:52, 18 October 2023

OCA — Wed, 18 Oct 2023 15:52:29 GMT

←Older revision		Revision as of 15:52, 18 October 2023
Line 1:		Line 1:

	==Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking==		==Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking==
-	<StructureSection load='7lk1' size='340' side='right'caption='[[7lk1]]' scene=''>	+	<StructureSection load='7lk1' size='340' side='right'caption='[[7lk1]], [[Resolution\|resolution]] 1.79Å' 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=7LK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7lk1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LK1 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=7lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lk1 OCA], [https://pdbe.org/7lk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lk1 RCSB], [https://www.ebi.ac.uk/pdbsum/7lk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lk1 ProSAT]</span></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]] 1.79Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=Y37:(1R,4R)-4-fluoro-3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-2-ene-1-carboxylic+acid'>Y37</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=7lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lk1 OCA], [https://pdbe.org/7lk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lk1 RCSB], [https://www.ebi.ac.uk/pdbsum/7lk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lk1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/OAT_HUMAN OAT_HUMAN] Defects in OAT are the cause of hyperornithinemia with gyrate atrophy of choroid and retina (HOGA) [MIM:[https://omim.org/entry/258870 258870]. HOGA is a slowly progressive blinding autosomal recessive disorder.<ref>PMID:3375240</ref> <ref>PMID:2793865</ref> <ref>PMID:1612597</ref> <ref>PMID:1737786</ref> <ref>PMID:7887415</ref> <ref>PMID:7668253</ref>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/OAT_HUMAN OAT_HUMAN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The inhibition of human ornithine delta-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.
		+
		+	Turnover and Inactivation Mechanisms for (S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase.,Shen S, Butrin A, Doubleday PF, Melani RD, Beaupre BA, Tavares MT, Ferreira GM, Kelleher NL, Moran GR, Liu D, Silverman RB J Am Chem Soc. 2021 Jun 16;143(23):8689-8703. doi: 10.1021/jacs.1c02456. Epub, 2021 Jun 7. PMID:34097381<ref>PMID:34097381</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7lk1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Butrin A]]		[[Category: Butrin A]]

OCA at 10:15, 16 February 2022

OCA — Wed, 16 Feb 2022 10:15:45 GMT

←Older revision		Revision as of 10:15, 16 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7lk1 is ON HOLD~~	+	==Ornithine Aminotransferase (OAT) with its potent inhibitor - (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) - 1 Hour Soaking==
-		+	<StructureSection load='7lk1' size='340' side='right'caption='[[7lk1]]' scene=''>
-	~~Authors: Butrin, A., Shen, S., Liu, D., Silverman, R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LK1 FirstGlance]. <br>
-	~~Description:~~ Ornithine Aminotransferase (OAT) with its potent inhibitor -(S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) -1 Hour Soaking	+	</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=7lk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lk1 OCA], [https://pdbe.org/7lk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lk1 RCSB], [https://www.ebi.ac.uk/pdbsum/7lk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lk1 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Liu~~, D]]	+	__TOC__
-	[[Category: ~~Shen, S~~]]	+	</StructureSection>
-	[[Category: Butrin, A]]	+	[[Category: Large Structures]]
-	[[Category: Silverman, R]]	+	[[Category: Butrin A]]
		+	[[Category: Liu D]]
		+	[[Category: Shen S]]
		+	[[Category: Silverman R]]

OCA: Protected "7lk1" [edit=sysop:move=sysop]

OCA — Wed, 10 Feb 2021 09:18:42 GMT

Protected "7lk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:18, 10 February 2021

OCA: New page: '''Unreleased structure''' The entry 7lk1 is ON HOLD Authors: Butrin, A., Shen, S., Liu, D., Silverman, R. Description: Ornithine Aminotransferase (OAT) with its potent inhibitor -(S)-...

OCA — Wed, 10 Feb 2021 09:18:41 GMT

New page: '''Unreleased structure''' The entry 7lk1 is ON HOLD Authors: Butrin, A., Shen, S., Liu, D., Silverman, R. Description: Ornithine Aminotransferase (OAT) with its potent inhibitor -(S)-...

New page

'''Unreleased structure'''

The entry 7lk1 is ON HOLD

Authors: Butrin, A., Shen, S., Liu, D., Silverman, R.

Description: Ornithine Aminotransferase (OAT) with its potent inhibitor -(S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148) -1 Hour Soaking
[[Category: Unreleased Structures]]
[[Category: Liu, D]]
[[Category: Shen, S]]
[[Category: Butrin, A]]
[[Category: Silverman, R]]