6f6t - Revision history

OCA at 10:22, 15 November 2023

2023-11-15T10:22:06Z

←Older revision		Revision as of 10:22, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='6f6t' size='340' side='right'caption='[[6f6t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6f6t' size='340' side='right'caption='[[6f6t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Petcr Petcr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Petroselinum_crispum Petroselinum crispum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F6T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CV2:(S)~~-(1~~-amino-2phenylallyl)phosphonic+acid'>CV2</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]] 1.8999597Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CV2:(S)-(1-amino-2phenylallyl)phosphonic+acid'>CV2</scene>, <scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4043 PETCR])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.24 4.3.1.24] </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=6f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6t OCA], [https://pdbe.org/6f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f6t RCSB], [https://www.ebi.ac.uk/pdbsum/6f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6t 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=6f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6t OCA], [https://pdbe.org/6f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f6t RCSB], [https://www.ebi.ac.uk/pdbsum/6f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PAL1_PETCR PAL1_PETCR]] This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.	+	[https://www.uniprot.org/uniprot/PAL1_PETCR PAL1_PETCR] This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Aromatic amino acid ammonia-lyases and aromatic amino acid 2,3-aminomutases contain the post-translationally formed prosthetic 3,5-dihydro-4-methylidene-5H-imidazol-5-one (MIO) group. MIO enzymes catalyze the stereoselective synthesis of alpha- or beta-amino acid enantiomers, making these chemical processes environmentally friendly and affordable. Characterization of novel inhibitors enables structural understanding of enzyme mechanism and recognizes promising herbicide candidates as well. The present study found that both enantiomers of the aminophosphonic acid analogue of the natural substrate phenylalanine and a novel derivative bearing a methylidene at the beta-position inhibited phenylalanine ammonia-lyases (PAL), representing MIO enzymes. X-ray methods unambiguously determined the absolute configuration of all tested enantiomers during their synthesis. Enzyme kinetic measurements revealed the enantiomer of the methylidene-substituted substrate analogue as being a mirror image relation to the natural l-phenylalanine as the strongest inhibitor. Isothermal titration calorimetry (ITC) confirmed the binding constants and provided a detailed analysis of the thermodynamic driving forces of ligand binding. Molecular docking suggested that binding of the (R)- and (S)-enantiomers is possible by a mirror image packing.	+
-		+
-	A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases.,Bata Z, Qian R, Roller A, Horak J, Bencze LC, Paizs C, Hammerschmidt F, Vertessy BG, Poppe L Adv Synth Catal. 2017 Jun 19;359(12):2109-2120. doi: 10.1002/adsc.201700428. Epub, 2017 May 19. PMID:28919846<ref>PMID:28919846</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6f6t" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Petcr]]~~	+	[[Category: Petroselinum crispum]]
-	~~[[Category: Phenylalanine ammonia-lyase~~]]	+	[[Category: Bata Z]]
-	[[Category: Bata, Z]]	+	[[Category: Leveles I]]
-	[[Category: Leveles, I]]	+	[[Category: Poppe L]]
-	[[Category: Poppe, L]]	+	[[Category: Vertessy GB]]
-	[[Category: Vertessy~~, G B]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:59, 7 April 2021

2021-04-07T06:59:27Z

←Older revision		Revision as of 06:59, 7 April 2021
Line 3:		Line 3:
	<StructureSection load='6f6t' size='340' side='right'caption='[[6f6t]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='6f6t' size='340' side='right'caption='[[6f6t]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6f6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6F6T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6f6t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Petcr Petcr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F6T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CV2:(S)-(1-amino-2phenylallyl)phosphonic+acid'>CV2</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CV2:(S)-(1-amino-2phenylallyl)phosphonic+acid'>CV2</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.24 4.3.1.24] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAL1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4043 PETCR])</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=6f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6t OCA], [~~http~~://pdbe.org/6f6t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6f6t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6f6t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6t ProSAT]</span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.24 4.3.1.24] </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=6f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6t OCA], [https://pdbe.org/6f6t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f6t RCSB], [https://www.ebi.ac.uk/pdbsum/6f6t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6t ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PAL1_PETCR PAL1_PETCR]] This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.	+	[[https://www.uniprot.org/uniprot/PAL1_PETCR PAL1_PETCR]] This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Petcr]]
	[[Category: Phenylalanine ammonia-lyase]]		[[Category: Phenylalanine ammonia-lyase]]
	[[Category: Bata, Z]]		[[Category: Bata, Z]]

OCA at 06:44, 26 June 2019

2019-06-26T06:44:49Z

←Older revision		Revision as of 06:44, 26 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6f6t is ~~ON HOLD until Paper~~ Publication	+	==Phenylalanine ammonia-lyase (PAL) from Petroselinum crispum complexed with S-APPA==
		+	<StructureSection load='6f6t' size='340' side='right'caption='[[6f6t]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6f6t]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F6T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CV2:(S)-(1-amino-2phenylallyl)phosphonic+acid'>CV2</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.24 4.3.1.24] </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=6f6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6t OCA], [http://pdbe.org/6f6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f6t RCSB], [http://www.ebi.ac.uk/pdbsum/6f6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6t ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAL1_PETCR PAL1_PETCR]] This is a key enzyme of plant metabolism catalyzing the first reaction in the biosynthesis from L-phenylalanine of a wide variety of natural products based on the phenylpropane skeleton.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aromatic amino acid ammonia-lyases and aromatic amino acid 2,3-aminomutases contain the post-translationally formed prosthetic 3,5-dihydro-4-methylidene-5H-imidazol-5-one (MIO) group. MIO enzymes catalyze the stereoselective synthesis of alpha- or beta-amino acid enantiomers, making these chemical processes environmentally friendly and affordable. Characterization of novel inhibitors enables structural understanding of enzyme mechanism and recognizes promising herbicide candidates as well. The present study found that both enantiomers of the aminophosphonic acid analogue of the natural substrate phenylalanine and a novel derivative bearing a methylidene at the beta-position inhibited phenylalanine ammonia-lyases (PAL), representing MIO enzymes. X-ray methods unambiguously determined the absolute configuration of all tested enantiomers during their synthesis. Enzyme kinetic measurements revealed the enantiomer of the methylidene-substituted substrate analogue as being a mirror image relation to the natural l-phenylalanine as the strongest inhibitor. Isothermal titration calorimetry (ITC) confirmed the binding constants and provided a detailed analysis of the thermodynamic driving forces of ligand binding. Molecular docking suggested that binding of the (R)- and (S)-enantiomers is possible by a mirror image packing.

-	~~Authors~~:	+	A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases.,Bata Z, Qian R, Roller A, Horak J, Bencze LC, Paizs C, Hammerschmidt F, Vertessy BG, Poppe L Adv Synth Catal. 2017 Jun 19;359(12):2109-2120. doi: 10.1002/adsc.201700428. Epub, 2017 May 19. PMID:28919846<ref>PMID:28919846</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6f6t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Phenylalanine ammonia-lyase]]
		+	[[Category: Bata, Z]]
		+	[[Category: Leveles, I]]
		+	[[Category: Poppe, L]]
		+	[[Category: Vertessy, G B]]
		+	[[Category: Complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Lyase]]

OCA at 05:14, 7 February 2018

2018-02-07T05:14:41Z

←Older revision		Revision as of 05:14, 7 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6f6t is ON HOLD	+	The entry 6f6t is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6f6t" [edit=sysop:move=sysop]

2017-12-13T06:03:06Z

Protected "6f6t" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:03, 13 December 2017

OCA: New page: '''Unreleased structure''' The entry 6f6t is ON HOLD Authors: Description: Category: Unreleased Structures

2017-12-13T06:03:05Z

New page: '''Unreleased structure''' The entry 6f6t is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6f6t is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]