5veq - Revision history

OCA at 10:06, 22 May 2024

OCA — Wed, 22 May 2024 10:06:08 GMT

←Older revision		Revision as of 10:06, 22 May 2024
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	<StructureSection load='5veq' size='340' side='right'caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='5veq' size='340' side='right'caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VEQ FirstGlance]. <br>
-	</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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]] 2.26Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e2y\|3e2y]]</div></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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kyat3, Ccbl2, Kat3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [https://pdbe.org/5veq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [https://www.ebi.ac.uk/pdbsum/5veq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq 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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [https://pdbe.org/5veq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [https://www.ebi.ac.uk/pdbsum/5veq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/KAT3_MOUSE KAT3_MOUSE]] Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro).<ref>PMID:19029248</ref>	+	[https://www.uniprot.org/uniprot/KAT3_MOUSE KAT3_MOUSE] Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro).<ref>PMID:19029248</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Kynurenine aminotransferase III (KAT III)~~ has ~~been considered to be involved in the production of mammalian brain kynurenic acid (KYNA)~~, ~~which plays an important role in protecting neurons from overstimulation~~ by ~~excitatory neurotransmitters. The enzyme was identified based on its high sequence identity with mammalian KAT I~~, but ~~its activity toward kynurenine and its structural characteristics have~~ not ~~been established~~. ~~In this study,~~ the ~~biochemical~~ and ~~structural properties of mouse KAT III (mKAT III)~~ were ~~determined. Specifically~~, ~~mKAT III cDNA was amplified from a mouse brain cDNA library~~, and ~~its recombinant protein was expressed in an insect cell protein expression system. We established that mKAT III is able~~ to ~~efficiently catalyze~~ the ~~transamination of kynurenine to KYNA and has optimum activity at relatively basic conditions of around pH 9.0 and at relatively high temperatures of 50 to 60 degrees C. In addition~~, ~~mKAT III~~ is ~~active toward a number~~ of ~~other amino acids. Its activity toward kynurenine is significantly decreased in~~ the ~~presence~~ of ~~methionine, histidine, glutamine, leucine, cysteine~~, and ~~3-hydroxykynurenine. Through macromolecular crystallography~~, ~~we determined~~ the ~~mKAT III crystal structure~~ and ~~its structures in complex with kynurenine and glutamine. Structural analysis revealed~~ the ~~overall architecture~~ of ~~mKAT III and its cofactor binding site and active center residues~~. ~~This is~~ the ~~first report concerning the biochemical characteristics~~ and ~~crystal structures~~ of ~~KAT III enzymes and provides~~ a ~~basis toward understanding the overall physiological role~~ of ~~mammalian KAT III in vivo~~ and ~~insight into regulating the levels of endogenous KYNA through modulation~~ of the ~~enzyme in~~ the ~~mouse brain~~.	+	The massive technical and computational progress of biomolecular crystallography has generated some adverse side effects. Most crystal structure models, produced by crystallographers or well-trained structural biologists, constitute useful sources of information, but occasional extreme outliers remind us that the process of structure determination is not fail-safe. The occurrence of severe errors or gross misinterpretations raises fundamental questions: Why do such aberrations emerge in the first place? How did they evade the sophisticated validation procedures which often produce clear and dire warnings, and why were severe errors not noticed by the depositors themselves, their supervisors, referees, and editors? Once detected, what can be done to either correct, improve, or eliminate such models? How do incorrect models affect the underlying claims or biomedical hypotheses they were intended, but failed, to support? What is the long-range effect of the propagation of such errors? And finally, what mechanisms can be envisioned to restore the validity of the scientific record and, if necessary, retract publications that are clearly invalidated by the lack of experimental evidence? We suggest that cognitive bias and flawed epistemology are likely at the root of the problem. By using examples from the published literature and from public repositories such as the Protein Data Bank, we provide case summaries to guide correction or improvement of structural models. When strong claims are unsustainable because of a deficient crystallographic model, removal of such a model and even retraction of the affected publication are necessary to restore the integrity of the scientific record. This article is protected by copyright. All rights reserved.

-	~~Biochemical and~~ structural ~~properties of mouse kynurenine aminotransferase III~~.,~~Han Q~~, ~~Robinson H~~, ~~Cai T~~, ~~Tagle DA~~, Li J ~~Mol Cell Biol~~. ~~2009 Feb;29(3)~~:~~784-93~~. ~~Epub 2008 Nov 24~~. PMID:~~19029248~~<ref>PMID:~~19029248~~</ref>	+	Detect, Correct, Retract: How to manage incorrect structural models.,Wlodawer A, Dauter Z, Porebski PJ, Minor W, Stanfield R, Jaskolski M, Pozharski E, Weichenberger CX, Rupp B FEBS J. 2017 Nov 7. doi: 10.1111/febs.14320. PMID:29113027<ref>PMID:29113027</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Dauter, Z]]	+	[[Category: Dauter Z]]
-	[[Category: Jaskolski, M]]	+	[[Category: Jaskolski M]]
-	[[Category: Minor, W]]	+	[[Category: Minor W]]
-	[[Category: Porebski, P]]	+	[[Category: Porebski P]]
-	[[Category: Pozharski, E]]	+	[[Category: Pozharski E]]
-	[[Category: Rupp, B]]	+	[[Category: Rupp B]]
-	[[Category: Stanfield, R]]	+	[[Category: Stanfield R]]
-	[[Category: Weichenberger~~, C X~~]]	+	[[Category: Weichenberger CX]]
-	[[Category: Wlodawer, A]]	+	[[Category: Wlodawer A]]
-	~~[[Category: Aminotransferase iii]]~~	+
-	~~[[Category: Mouse]]~~	+
-	~~[[Category: Re-refinement]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:14, 13 April 2022

OCA — Wed, 13 Apr 2022 10:14:48 GMT

←Older revision		Revision as of 10:14, 13 April 2022
Line 1:		Line 1:

	==MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y==		==MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y==
-	<StructureSection load='5veq' size='340' side='right' caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>	+	<StructureSection load='5veq' size='340' side='right'caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VEQ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>	+	</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e2y\|3e2y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e2y\|3e2y]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kyat3, Ccbl2, Kat3 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kyat3, Ccbl2, Kat3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [~~http~~://pdbe.org/5veq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5veq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq 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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [https://pdbe.org/5veq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [https://www.ebi.ac.uk/pdbsum/5veq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/KAT3_MOUSE KAT3_MOUSE]] Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro).<ref>PMID:19029248</ref>	+	[[https://www.uniprot.org/uniprot/KAT3_MOUSE KAT3_MOUSE]] Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro).<ref>PMID:19029248</ref>
	<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 5veq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5veq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminotransferase 3D structures\|Aminotransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]

OCA at 06:59, 15 February 2018

OCA — Thu, 15 Feb 2018 06:59:35 GMT

←Older revision		Revision as of 06:59, 15 February 2018
Line 3:		Line 3:
	<StructureSection load='5veq' size='340' side='right' caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>		<StructureSection load='5veq' size='340' side='right' caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEQ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e2y\|3e2y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e2y\|3e2y]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Kyat3, Ccbl2, Kat3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [http://pdbe.org/5veq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [http://www.ebi.ac.uk/pdbsum/5veq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq 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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [http://pdbe.org/5veq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [http://www.ebi.ac.uk/pdbsum/5veq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]
	[[Category: Jaskolski, M]]		[[Category: Jaskolski, M]]

OCA at 06:11, 29 November 2017

OCA — Wed, 29 Nov 2017 06:11:31 GMT

←Older revision		Revision as of 06:11, 29 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5veq is ~~ON HOLD~~	+	==MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y==
		+	<StructureSection load='5veq' size='340' side='right' caption='[[5veq]], [[Resolution\|resolution]] 2.26Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5veq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VEQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VEQ 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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PMP:4-DEOXY-4-AMINOPYRIDOXAL-5-PHOSPHATE'>PMP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e2y\|3e2y]]</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=5veq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5veq OCA], [http://pdbe.org/5veq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5veq RCSB], [http://www.ebi.ac.uk/pdbsum/5veq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5veq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KAT3_MOUSE KAT3_MOUSE]] Catalyzes the irreversible transamination of the L-tryptophan metabolite L-kynurenine to form kynurenic acid (KA). May catalyze the beta-elimination of S-conjugates and Se-conjugates of L-(seleno)cysteine, resulting in the cleavage of the C-S or C-Se bond (By similarity). Has transaminase activity towards L-kynurenine, tryptophan, phenylalanine, serine, cysteine, methionine, histidine, glutamine and asparagine with glyoxylate as an amino group acceptor (in vitro). Has lower activity with 2-oxoglutarate as amino group acceptor (in vitro).<ref>PMID:19029248</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Kynurenine aminotransferase III (KAT III) has been considered to be involved in the production of mammalian brain kynurenic acid (KYNA), which plays an important role in protecting neurons from overstimulation by excitatory neurotransmitters. The enzyme was identified based on its high sequence identity with mammalian KAT I, but its activity toward kynurenine and its structural characteristics have not been established. In this study, the biochemical and structural properties of mouse KAT III (mKAT III) were determined. Specifically, mKAT III cDNA was amplified from a mouse brain cDNA library, and its recombinant protein was expressed in an insect cell protein expression system. We established that mKAT III is able to efficiently catalyze the transamination of kynurenine to KYNA and has optimum activity at relatively basic conditions of around pH 9.0 and at relatively high temperatures of 50 to 60 degrees C. In addition, mKAT III is active toward a number of other amino acids. Its activity toward kynurenine is significantly decreased in the presence of methionine, histidine, glutamine, leucine, cysteine, and 3-hydroxykynurenine. Through macromolecular crystallography, we determined the mKAT III crystal structure and its structures in complex with kynurenine and glutamine. Structural analysis revealed the overall architecture of mKAT III and its cofactor binding site and active center residues. This is the first report concerning the biochemical characteristics and crystal structures of KAT III enzymes and provides a basis toward understanding the overall physiological role of mammalian KAT III in vivo and insight into regulating the levels of endogenous KYNA through modulation of the enzyme in the mouse brain.

-	~~Authors: Wlodawer, A~~., ~~Dauter~~, Z., ~~Minor~~, W., ~~Stanfield, R~~.~~, Porebski, P~~.~~, Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B~~.	+	Biochemical and structural properties of mouse kynurenine aminotransferase III.,Han Q, Robinson H, Cai T, Tagle DA, Li J Mol Cell Biol. 2009 Feb;29(3):784-93. Epub 2008 Nov 24. PMID:19029248<ref>PMID:19029248</ref>

-	~~Description: MOUSE KYNURENINE AMINOTRANSFERASE III~~, ~~RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5veq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]
-	[[Category: ~~Rupp~~, B]]	+	[[Category: Jaskolski, M]]
		+	[[Category: Minor, W]]
	[[Category: Porebski, P]]		[[Category: Porebski, P]]
-	[[Category: Weichenberger, C.X]]
	[[Category: Pozharski, E]]		[[Category: Pozharski, E]]
-	[[Category: ~~Wlodawer~~, ~~A]]~~	+	[[Category: Rupp, B]]
-	~~[[Category: Minor, W]]~~	+
-	~~[[Category: Jaskolski, M~~]]	+
	[[Category: Stanfield, R]]		[[Category: Stanfield, R]]
		+	[[Category: Weichenberger, C X]]
		+	[[Category: Wlodawer, A]]
		+	[[Category: Aminotransferase iii]]
		+	[[Category: Mouse]]
		+	[[Category: Re-refinement]]
		+	[[Category: Transferase]]

OCA at 11:21, 19 April 2017

OCA — Wed, 19 Apr 2017 11:21:04 GMT

←Older revision		Revision as of 11:21, 19 April 2017
Line 3:		Line 3:
	The entry 5veq is ON HOLD		The entry 5veq is ON HOLD

-	Authors: A. ~~Wlodawer~~, Z. ~~Dauter~~, W. ~~Minor~~, R. ~~Stanfield~~, P. ~~Porebski~~, M. ~~Jaskolski~~, E. ~~Pozharski~~, C.X. ~~Weichenberger~~, B. ~~Rupp~~	+	Authors: Wlodawer, A., Dauter, Z., Minor, W., Stanfield, R., Porebski, P., Jaskolski, M., Pozharski, E., Weichenberger, C.X., Rupp, B.

-	Description: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE ~~3E2F~~	+	Description: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Y
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~A. Wlodawer~~, Z~~. Dauter~~, ~~W. Minor, R. Stanfield~~, P~~. Porebski~~, M. ~~Jaskolski~~, E~~. Pozharski~~, ~~C.X. Weichenberger~~, ~~B. Rupp~~]]	+	[[Category: Dauter, Z]]
		+	[[Category: Rupp, B]]
		+	[[Category: Porebski, P]]
		+	[[Category: Weichenberger, C.X]]
		+	[[Category: Pozharski, E]]
		+	[[Category: Wlodawer, A]]
		+	[[Category: Minor, W]]
		+	[[Category: Jaskolski, M]]
		+	[[Category: Stanfield, R]]

OCA: Protected "5veq" [edit=sysop:move=sysop]

OCA — Wed, 12 Apr 2017 09:59:11 GMT

Protected "5veq" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:59, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5veq is ON HOLD Authors: A. Wlodawer, Z. Dauter, W. Minor, R. Stanfield, P. Porebski, M. Jaskolski, E. Pozharski, C.X. Weichenberger, B. Rupp Descr...

OCA — Wed, 12 Apr 2017 09:59:10 GMT

New page: '''Unreleased structure''' The entry 5veq is ON HOLD Authors: A. Wlodawer, Z. Dauter, W. Minor, R. Stanfield, P. Porebski, M. Jaskolski, E. Pozharski, C.X. Weichenberger, B. Rupp Descr...

New page

'''Unreleased structure'''

The entry 5veq is ON HOLD

Authors: A. Wlodawer, Z. Dauter, W. Minor, R. Stanfield, P. Porebski, M. Jaskolski, E. Pozharski, C.X. Weichenberger, B. Rupp

Description: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F
[[Category: Unreleased Structures]]
[[Category: A. Wlodawer, Z. Dauter, W. Minor, R. Stanfield, P. Porebski, M. Jaskolski, E. Pozharski, C.X. Weichenberger, B. Rupp]]