6liv - Revision history

OCA at 07:35, 1 May 2024

OCA — Wed, 01 May 2024 07:35:51 GMT

←Older revision		Revision as of 07:35, 1 May 2024
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	<StructureSection load='6liv' size='340' side='right'caption='[[6liv]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='6liv' size='340' side='right'caption='[[6liv]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6liv]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LIV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6LIV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6liv]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Papaver_somniferum Papaver somniferum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LIV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LIV FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</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]] 2.31Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=6liv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6liv OCA], [~~http~~://pdbe.org/6liv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6liv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6liv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6liv 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=6liv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6liv OCA], [https://pdbe.org/6liv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6liv RCSB], [https://www.ebi.ac.uk/pdbsum/6liv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6liv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TYDC2_PAPSO TYDC2_PAPSO]] Marginally higher substrate specificity for L-DOPA over L-tyrosine.	+	[https://www.uniprot.org/uniprot/TYDC2_PAPSO TYDC2_PAPSO] Marginally higher substrate specificity for L-DOPA over L-tyrosine.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Plant tyrosine decarboxylase (TyrDC) is a group II pyridoxal 5'-phosphate (PLP)-dependent decarboxylase that mainly catalyzes the decarboxylation of tyrosine to tyramine. This is biologically important for diverting essential primary metabolites into secondary metabolic pathways. Intensive studies have characterized the effective of PLP-binding and the substrate specificity of mammalian 3,4-dihydroxyphenyl-l-alanine (Dopa) decarboxylases, a member of group II PLP-dependent decarboxylase. However, the characteristics of PLP binding and substrate specificity of plant TyrDCs remain unknown. In this study, we focus on the PLP binding manner, and determined the crystal structures of the apo and PLP binding form of type II TyrDC from Papaver somniferum (PsTyrDCII and PsTyrDCII-PLP). The structures showed that, unlike mammalian Dopa decarboxylase, the binding of PLP does not induce distinct conformational changes of PsTyrDCII regarding the overall structure, but the PLP binding pocket displays conformational changes at Phe124, His203 and Thr262. Combining structural comparation and the obtained biochemical findings, it is demonstrated that PsTyrDCII does not binds PLP tightly. Such characteristics of PLP binding may be required by its catalytic reaction and substrate binding. The activity of TyrDC probably regulated by the concentration of PLP in cells.	+

-	Crystal structures clarify cofactor binding of plant tyrosine decarboxylase.,Wang H, Yu J, Satoh Y, Nakagawa Y, Tanaka R, Kato K, Yao M Biochem Biophys Res Commun. 2020 Mar 5;523(2):500-505. doi:, 10.1016/j.bbrc.2019.12.077. Epub 2019 Dec 30. PMID:31898973<ref>PMID:31898973</ref>	+	==See Also==
-		+	*[[DOPA decarboxylase\|DOPA decarboxylase]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6liv" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Wang, H~~]]	+	[[Category: Papaver somniferum]]
-	[[Category: ~~Yao, M~~]]	+	[[Category: Wang H]]
-	[[Category: ~~Yu, J~~]]	+	[[Category: Yao M]]
-	[[Category: ~~Decarboxylase]]~~	+	[[Category: Yu J]]
-	~~[[Category: Holo form]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Plp binding]]~~	+
-	~~[[Category: Tyrosine~~]]	+

OCA at 04:15, 13 February 2020

OCA — Thu, 13 Feb 2020 04:15:11 GMT

←Older revision		Revision as of 04:15, 13 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6liv is ~~ON HOLD~~	+	==Crystal structure of Tyrosine decarboxylase in complex with PLP==
		+	<StructureSection load='6liv' size='340' side='right'caption='[[6liv]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6liv]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LIV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6LIV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=6liv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6liv OCA], [http://pdbe.org/6liv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6liv RCSB], [http://www.ebi.ac.uk/pdbsum/6liv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6liv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYDC2_PAPSO TYDC2_PAPSO]] Marginally higher substrate specificity for L-DOPA over L-tyrosine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Plant tyrosine decarboxylase (TyrDC) is a group II pyridoxal 5'-phosphate (PLP)-dependent decarboxylase that mainly catalyzes the decarboxylation of tyrosine to tyramine. This is biologically important for diverting essential primary metabolites into secondary metabolic pathways. Intensive studies have characterized the effective of PLP-binding and the substrate specificity of mammalian 3,4-dihydroxyphenyl-l-alanine (Dopa) decarboxylases, a member of group II PLP-dependent decarboxylase. However, the characteristics of PLP binding and substrate specificity of plant TyrDCs remain unknown. In this study, we focus on the PLP binding manner, and determined the crystal structures of the apo and PLP binding form of type II TyrDC from Papaver somniferum (PsTyrDCII and PsTyrDCII-PLP). The structures showed that, unlike mammalian Dopa decarboxylase, the binding of PLP does not induce distinct conformational changes of PsTyrDCII regarding the overall structure, but the PLP binding pocket displays conformational changes at Phe124, His203 and Thr262. Combining structural comparation and the obtained biochemical findings, it is demonstrated that PsTyrDCII does not binds PLP tightly. Such characteristics of PLP binding may be required by its catalytic reaction and substrate binding. The activity of TyrDC probably regulated by the concentration of PLP in cells.

-	~~Authors~~:	+	Crystal structures clarify cofactor binding of plant tyrosine decarboxylase.,Wang H, Yu J, Satoh Y, Nakagawa Y, Tanaka R, Kato K, Yao M Biochem Biophys Res Commun. 2020 Mar 5;523(2):500-505. doi:, 10.1016/j.bbrc.2019.12.077. Epub 2019 Dec 30. PMID:31898973<ref>PMID:31898973</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6liv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Wang, H]]
		+	[[Category: Yao, M]]
		+	[[Category: Yu, J]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Holo form]]
		+	[[Category: Lyase]]
		+	[[Category: Plp binding]]
		+	[[Category: Tyrosine]]

OCA: Protected "6liv" [edit=sysop:move=sysop]

OCA — Wed, 18 Dec 2019 05:45:00 GMT

Protected "6liv" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:45, 18 December 2019

OCA: New page: '''Unreleased structure''' The entry 6liv is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Dec 2019 05:44:58 GMT

New page: '''Unreleased structure''' The entry 6liv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6liv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]