5hsi - Revision history

OCA at 09:15, 20 March 2024

2024-03-20T09:15:58Z

←Older revision		Revision as of 09:15, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TYRDC_LEVBR TYRDC_LEVBR] Catalyzes the decarboxylation of L-tyrosine to produce tyramine (PubMed:24211777, PubMed:27292129). Cannot use other aromatic L-amino acids as substrates like L-phenylalanine, L-tryptophan and L-glutamate (PubMed:24211777).<ref>PMID:24211777</ref> <ref>PMID:27292129</ref> Is also able to decarboxylate the Parkinson's disease medication levodopa (L-dopa) to dopamine in vitro.<ref>PMID:24211777</ref> <ref>PMID:27292129</ref>		[https://www.uniprot.org/uniprot/TYRDC_LEVBR TYRDC_LEVBR] Catalyzes the decarboxylation of L-tyrosine to produce tyramine (PubMed:24211777, PubMed:27292129). Cannot use other aromatic L-amino acids as substrates like L-phenylalanine, L-tryptophan and L-glutamate (PubMed:24211777).<ref>PMID:24211777</ref> <ref>PMID:27292129</ref> Is also able to decarboxylate the Parkinson's disease medication levodopa (L-dopa) to dopamine in vitro.<ref>PMID:24211777</ref> <ref>PMID:27292129</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Tyrosine decarboxylase (TDC) is a pyridoxal 5-phosphate (PLP)-dependent enzyme and is mainly responsible for the synthesis of tyramine, an important biogenic amine. In this study, the crystal structures of the apo and holo forms of Lactobacillus brevis TDC (LbTDC) were determined. The LbTDC displays only 25% sequence identity with the only reported TDC structure. Site-directed mutagenesis of the conformationally flexible sites and catalytic center was performed to investigate the potential catalytic mechanism. It was found that H241 in the active site plays an important role in PLP binding because it has different conformations in the apo and holo structures of LbTDC. After binding to PLP, H241 rotated to the position adjacent to the PLP pyridine ring. Alanine scanning mutagenesis revealed several crucial regions that determine the substrate specificity and catalytic activity. Among the mutants, the S586A variant displayed increased catalytic efficiency and substrate affinity, which is attributed to decreased steric hindrance and increased hydrophobicity, as verified by the saturation mutagenesis at S586. Our results provide structural information about the residues important for the protein engineering of TDC to improve catalytic efficiency in the green manufacturing of tyramine.
-
-	Crystal structure of tyrosine decarboxylase and identification of key residues involved in conformational swing and substrate binding.,Zhu H, Xu G, Zhang K, Kong X, Han R, Zhou J, Ni Y Sci Rep. 2016 Jun 13;6:27779. doi: 10.1038/srep27779. PMID:27292129<ref>PMID:27292129</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5hsi" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:52, 16 August 2023

2023-08-16T10:52:50Z

←Older revision		Revision as of 10:52, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='5hsi' size='340' side='right'caption='[[5hsi]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='5hsi' size='340' side='right'caption='[[5hsi]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hsi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_casei_g"_von_freudenreich_and_thoni_1904 "bacillus casei g" von freudenreich and thoni 1904~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5HSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hsi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Levilactobacillus_brevis Levilactobacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HSI FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.732Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5hsj\|5hsj~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>tdc, N624_0219 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1580~~ "~~Bacillus casei g~~" ~~von Freudenreich and Thoni 1904])</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=5hsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsi OCA], [https://pdbe.org/5hsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hsi RCSB], [https://www.ebi.ac.uk/pdbsum/5hsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsi ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Tyrosine_decarboxylase Tyrosine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.25 4.1.1.25]~~ </~~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=5hsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsi OCA], [~~http~~://pdbe.org/5hsi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5hsi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5hsi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsi ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/TYRDC_LEVBR TYRDC_LEVBR] Catalyzes the decarboxylation of L-tyrosine to produce tyramine (PubMed:24211777, PubMed:27292129). Cannot use other aromatic L-amino acids as substrates like L-phenylalanine, L-tryptophan and L-glutamate (PubMed:24211777).<ref>PMID:24211777</ref> <ref>PMID:27292129</ref> Is also able to decarboxylate the Parkinson's disease medication levodopa (L-dopa) to dopamine in vitro.<ref>PMID:24211777</ref> <ref>PMID:27292129</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus casei g von freudenreich and thoni 1904]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Tyrosine decarboxylase~~]]	+	[[Category: Levilactobacillus brevis]]
-	[[Category: Ni, Y]]	+	[[Category: Ni Y]]
-	[[Category: Zhang, K]]	+	[[Category: Zhang K]]
-	[[Category: Zhou, J]]	+	[[Category: Zhou J]]
-	[[Category: Zhu, H]]	+	[[Category: Zhu H]]
-	~~[[Category: L-tyrosine decarboxylase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:16, 19 February 2020

2020-02-19T07:16:25Z

←Older revision		Revision as of 07:16, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of tyrosine decarboxylase at 1.73 Angstroms resolution==		==Crystal structure of tyrosine decarboxylase at 1.73 Angstroms resolution==
-	<StructureSection load='5hsi' size='340' side='right' caption='[[5hsi]], [[Resolution\|resolution]] 1.73Å' scene=''>	+	<StructureSection load='5hsi' size='340' side='right'caption='[[5hsi]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5hsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HSI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5hsi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_casei_g"_von_freudenreich_and_thoni_1904 "bacillus casei g" von freudenreich and thoni 1904]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HSI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hsj\|5hsj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hsj\|5hsj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tdc, N624_0219 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1580 "Bacillus casei g" von Freudenreich and Thoni 1904])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_decarboxylase Tyrosine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.25 4.1.1.25] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_decarboxylase Tyrosine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.25 4.1.1.25] </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=5hsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsi OCA], [http://pdbe.org/5hsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsi RCSB], [http://www.ebi.ac.uk/pdbsum/5hsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsi 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=5hsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsi OCA], [http://pdbe.org/5hsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsi RCSB], [http://www.ebi.ac.uk/pdbsum/5hsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsi ProSAT]</span></td></tr>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus casei g von freudenreich and thoni 1904]]
		+	[[Category: Large Structures]]
	[[Category: Tyrosine decarboxylase]]		[[Category: Tyrosine decarboxylase]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]

OCA at 13:50, 21 September 2016

2016-09-21T13:50:57Z

←Older revision		Revision as of 13:50, 21 September 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5hsi is ~~ON HOLD~~	+	==Crystal structure of tyrosine decarboxylase at 1.73 Angstroms resolution==
		+	<StructureSection load='5hsi' size='340' side='right' caption='[[5hsi]], [[Resolution\|resolution]] 1.73Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5hsi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HSI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HSI FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hsj\|5hsj]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine_decarboxylase Tyrosine decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.25 4.1.1.25] </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=5hsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hsi OCA], [http://pdbe.org/5hsi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hsi RCSB], [http://www.ebi.ac.uk/pdbsum/5hsi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hsi ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tyrosine decarboxylase (TDC) is a pyridoxal 5-phosphate (PLP)-dependent enzyme and is mainly responsible for the synthesis of tyramine, an important biogenic amine. In this study, the crystal structures of the apo and holo forms of Lactobacillus brevis TDC (LbTDC) were determined. The LbTDC displays only 25% sequence identity with the only reported TDC structure. Site-directed mutagenesis of the conformationally flexible sites and catalytic center was performed to investigate the potential catalytic mechanism. It was found that H241 in the active site plays an important role in PLP binding because it has different conformations in the apo and holo structures of LbTDC. After binding to PLP, H241 rotated to the position adjacent to the PLP pyridine ring. Alanine scanning mutagenesis revealed several crucial regions that determine the substrate specificity and catalytic activity. Among the mutants, the S586A variant displayed increased catalytic efficiency and substrate affinity, which is attributed to decreased steric hindrance and increased hydrophobicity, as verified by the saturation mutagenesis at S586. Our results provide structural information about the residues important for the protein engineering of TDC to improve catalytic efficiency in the green manufacturing of tyramine.

-	~~Authors: Ni, Y., Zhou, J~~., Zhu, H., ~~Zhang~~, K.	+	Crystal structure of tyrosine decarboxylase and identification of key residues involved in conformational swing and substrate binding.,Zhu H, Xu G, Zhang K, Kong X, Han R, Zhou J, Ni Y Sci Rep. 2016 Jun 13;6:27779. doi: 10.1038/srep27779. PMID:27292129<ref>PMID:27292129</ref>

-	~~Description: Crystal structure~~ of ~~tyrosine decarboxylase at 1~~.~~73 Angstroms resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5hsi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Tyrosine decarboxylase]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]
	[[Category: Zhang, K]]		[[Category: Zhang, K]]
-	[[Category: Zhu, H]]
	[[Category: Zhou, J]]		[[Category: Zhou, J]]
		+	[[Category: Zhu, H]]
		+	[[Category: L-tyrosine decarboxylase]]
		+	[[Category: Lyase]]

OCA at 10:48, 14 September 2016

2016-09-14T10:48:47Z

←Older revision		Revision as of 10:48, 14 September 2016
Line 5:		Line 5:
	Authors: Ni, Y., Zhou, J., Zhu, H., Zhang, K.		Authors: Ni, Y., Zhou, J., Zhu, H., Zhang, K.

-	Description: ~~Structure~~ of tyrosine decarboxylase at 1.73 Angstroms resolution	+	Description: Crystal structure of tyrosine decarboxylase at 1.73 Angstroms resolution
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ni, Y]]		[[Category: Ni, Y]]

OCA at 15:40, 10 February 2016

2016-02-10T15:40:05Z

←Older revision		Revision as of 15:40, 10 February 2016
Line 3:		Line 3:
	The entry 5hsi is ON HOLD		The entry 5hsi is ON HOLD

-	Authors: Ye Ni, ~~Jia-hai~~ Zhou, ~~Hai-xia~~ Zhu, ~~Kai~~ Zhang	+	Authors: Ni, Y., Zhou, J., Zhu, H., Zhang, K.

	Description: Structure of tyrosine decarboxylase at 1.73 Angstroms resolution		Description: Structure of tyrosine decarboxylase at 1.73 Angstroms resolution
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ye Ni, ~~Jia-Hai Zhou~~, ~~Hai-Xia~~ Zhu, ~~Kai Zhang~~]]	+	[[Category: Ni, Y]]
		+	[[Category: Zhang, K]]
		+	[[Category: Zhu, H]]
		+	[[Category: Zhou, J]]

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

2016-02-03T14:16:32Z

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

←Older revision

Revision as of 14:16, 3 February 2016

OCA: New page: '''Unreleased structure''' The entry 5hsi is ON HOLD Authors: Ye Ni, Jia-hai Zhou, Hai-xia Zhu, Kai Zhang Description: Structure of tyrosine decarboxylase at 1.73 Angstroms resolution ...

2016-02-03T14:16:31Z

New page: '''Unreleased structure''' The entry 5hsi is ON HOLD Authors: Ye Ni, Jia-hai Zhou, Hai-xia Zhu, Kai Zhang Description: Structure of tyrosine decarboxylase at 1.73 Angstroms resolution ...

New page

'''Unreleased structure'''

The entry 5hsi is ON HOLD

Authors: Ye Ni, Jia-hai Zhou, Hai-xia Zhu, Kai Zhang

Description: Structure of tyrosine decarboxylase at 1.73 Angstroms resolution
[[Category: Unreleased Structures]]
[[Category: Ye Ni, Jia-Hai Zhou, Hai-Xia Zhu, Kai Zhang]]