5ver - Revision history

OCA at 10:14, 13 April 2022

OCA — Wed, 13 Apr 2022 10:14:51 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 3E2Z==		==MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Z==
-	<StructureSection load='5ver' size='340' side='right' caption='[[5ver]], [[Resolution\|resolution]] 2.81Å' scene=''>	+	<StructureSection load='5ver' size='340' side='right'caption='[[5ver]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ver]] 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=5VER OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VER FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ver]] 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=5VER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VER 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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">[[3e2z\|3e2z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e2z\|3e2z]]</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=5ver FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ver OCA], [~~http~~://pdbe.org/5ver PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ver RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ver PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ver 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=5ver FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ver OCA], [https://pdbe.org/5ver PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ver RCSB], [https://www.ebi.ac.uk/pdbsum/5ver PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ver 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 ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5ver" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ver" 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 06:59:39 GMT

←Older revision		Revision as of 06:59, 15 February 2018
Line 3:		Line 3:
	<StructureSection load='5ver' size='340' side='right' caption='[[5ver]], [[Resolution\|resolution]] 2.81Å' scene=''>		<StructureSection load='5ver' size='340' side='right' caption='[[5ver]], [[Resolution\|resolution]] 2.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ver]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VER FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ver]] 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=5VER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VER 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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">[[3e2z\|3e2z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3e2z\|3e2z]]</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=5ver FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ver OCA], [http://pdbe.org/5ver PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ver RCSB], [http://www.ebi.ac.uk/pdbsum/5ver PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ver 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=5ver FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ver OCA], [http://pdbe.org/5ver PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ver RCSB], [http://www.ebi.ac.uk/pdbsum/5ver PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ver ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__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 06:11:33 GMT

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

-	~~The entry~~ 5ver is ~~ON HOLD~~	+	==MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Z==
		+	<StructureSection load='5ver' size='340' side='right' caption='[[5ver]], [[Resolution\|resolution]] 2.81Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ver]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VER OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VER 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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">[[3e2z\|3e2z]]</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=5ver FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ver OCA], [http://pdbe.org/5ver PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ver RCSB], [http://www.ebi.ac.uk/pdbsum/5ver PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ver 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 3E2Z~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
		+	<div class="pdbe-citations 5ver" 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 11:21:07 GMT

←Older revision		Revision as of 11:21, 19 April 2017
Line 3:		Line 3:
	The entry 5ver is ON HOLD		The entry 5ver 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 3E2Z		Description: MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Z
	[[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 "5ver" [edit=sysop:move=sysop]

OCA — Wed, 12 Apr 2017 09:59:14 GMT

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

←Older revision

Revision as of 09:59, 12 April 2017

OCA: New page: '''Unreleased structure''' The entry 5ver 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 09:59:12 GMT

New page: '''Unreleased structure''' The entry 5ver 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 5ver 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 3E2Z
[[Category: Unreleased Structures]]
[[Category: A. Wlodawer, Z. Dauter, W. Minor, R. Stanfield, P. Porebski, M. Jaskolski, E. Pozharski, C.X. Weichenberger, B. Rupp]]