5n81 - Revision history

OCA at 12:33, 15 November 2023

OCA — Wed, 15 Nov 2023 12:33:12 GMT

←Older revision		Revision as of 12:33, 15 November 2023
Line 1:		Line 1:

	==Crystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog==		==Crystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog==
-	<StructureSection load='5n81' size='340' side='right' caption='[[5n81]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5n81' size='340' side='right'caption='[[5n81]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n81]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_10027 Atcc 10027~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N81 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5N81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n81]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_parabrevis Brevibacillus parabrevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N81 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N81 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q2:[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate'>8Q2</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.6Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 ATCC 10027])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8Q2:[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate'>8Q2</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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_racemase_(ATP-hydrolyzing) Phenylalanine racemase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.11 5.1.1.11] </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=5n81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n81 OCA], [https://pdbe.org/5n81 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n81 RCSB], [https://www.ebi.ac.uk/pdbsum/5n81 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n81 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=5n81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n81 OCA], [~~http~~://pdbe.org/5n81 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5n81 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5n81 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5n81 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TYCA_BREPA TYCA_BREPA]] In the first step of peptide synthesis this enzyme activates phenylalanine and racemizes it to the D-isomer.	+	[https://www.uniprot.org/uniprot/TYCA_BREPA TYCA_BREPA] In the first step of peptide synthesis this enzyme activates phenylalanine and racemizes it to the D-isomer.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 10027~~]]	+	[[Category: Brevibacillus parabrevis]]
-	[[Category: Fercher, D]]	+	[[Category: Large Structures]]
-	[[Category: Hansen~~, D A~~]]	+	[[Category: Fercher D]]
-	[[Category: Hilvert, D]]	+	[[Category: Hansen DA]]
-	[[Category: Kries, H]]	+	[[Category: Hilvert D]]
-	[[Category: Mori, T]]	+	[[Category: Kries H]]
-	[[Category: Niquille~~, D L]]~~	+	[[Category: Mori T]]
-	~~[[Category: Adenylation domain]]~~	+	[[Category: Niquille DL]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Nonribosomal peptide synthetase~~]]	+

OCA at 07:07, 28 February 2018

OCA — Wed, 28 Feb 2018 07:07:38 GMT

←Older revision		Revision as of 07:07, 28 February 2018
Line 3:		Line 3:
	<StructureSection load='5n81' size='340' side='right' caption='[[5n81]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5n81' size='340' side='right' caption='[[5n81]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5n81]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N81 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5n81]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_10027 Atcc 10027]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N81 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q2:[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate'>8Q2</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q2:[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate'>8Q2</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tycA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=54914 ATCC 10027])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine_racemase_(ATP-hydrolyzing) Phenylalanine racemase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.11 5.1.1.11] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine_racemase_(ATP-hydrolyzing) Phenylalanine racemase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.11 5.1.1.11] </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=5n81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n81 OCA], [http://pdbe.org/5n81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n81 RCSB], [http://www.ebi.ac.uk/pdbsum/5n81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n81 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=5n81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n81 OCA], [http://pdbe.org/5n81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n81 RCSB], [http://www.ebi.ac.uk/pdbsum/5n81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n81 ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TYCA_BREPA TYCA_BREPA]] In the first step of peptide synthesis this enzyme activates phenylalanine and racemizes it to the D-isomer.		[[http://www.uniprot.org/uniprot/TYCA_BREPA TYCA_BREPA]] In the first step of peptide synthesis this enzyme activates phenylalanine and racemizes it to the D-isomer.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-beta-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold alpha/beta-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-beta-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l(-1)), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal beta-frameworks.
		+
		+	Nonribosomal biosynthesis of backbone-modified peptides.,Niquille DL, Hansen DA, Mori T, Fercher D, Kries H, Hilvert D Nat Chem. 2018 Mar;10(3):282-287. doi: 10.1038/nchem.2891. Epub 2017 Nov 20. PMID:29461527<ref>PMID:29461527</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5n81" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 10027]]
	[[Category: Fercher, D]]		[[Category: Fercher, D]]
	[[Category: Hansen, D A]]		[[Category: Hansen, D A]]

OCA at 06:54, 13 December 2017

OCA — Wed, 13 Dec 2017 06:54:40 GMT

←Older revision		Revision as of 06:54, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5n81 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog==
-		+	<StructureSection load='5n81' size='340' side='right' caption='[[5n81]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~: ~~Niquille, D~~.L.~~, Hansen, D~~.A., ~~Mori~~, T., ~~Fercher~~, D., ~~Kries~~, H., ~~Hilvert, D~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5n81]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N81 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5N81 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of an engineered TycA variant in complex with an O~~-~~propargyl~~-~~beta~~-~~Tyr-AMP analog~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8Q2:[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+~{N}-[(3~{S})-3-azanyl-3-(4-prop-2-ynoxyphenyl)propanoyl]sulfamate'>8Q2</scene>, <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine_racemase_(ATP-hydrolyzing) Phenylalanine racemase (ATP-hydrolyzing)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.11 5.1.1.11] </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=5n81 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n81 OCA], [http://pdbe.org/5n81 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5n81 RCSB], [http://www.ebi.ac.uk/pdbsum/5n81 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5n81 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYCA_BREPA TYCA_BREPA]] In the first step of peptide synthesis this enzyme activates phenylalanine and racemizes it to the D-isomer.
		+	__TOC__
		+	</StructureSection>
	[[Category: Fercher, D]]		[[Category: Fercher, D]]
-	[[Category: ~~Mori~~, T]]	+	[[Category: Hansen, D A]]
	[[Category: Hilvert, D]]		[[Category: Hilvert, D]]
	[[Category: Kries, H]]		[[Category: Kries, H]]
-	[[Category: ~~Hansen~~, ~~D.A~~]]	+	[[Category: Mori, T]]
-	[[Category: Niquille, D.L]]	+	[[Category: Niquille, D L]]
		+	[[Category: Adenylation domain]]
		+	[[Category: Ligase]]
		+	[[Category: Nonribosomal peptide synthetase]]

OCA: Protected "5n81" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 12:14:37 GMT

Protected "5n81" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:14, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5n81 is ON HOLD until Paper Publication Authors: Niquille, D.L., Hansen, D.A., Mori, T., Fercher, D., Kries, H., Hilvert, D. Description: Crystal s...

OCA — Thu, 09 Mar 2017 12:14:35 GMT

New page: '''Unreleased structure''' The entry 5n81 is ON HOLD until Paper Publication Authors: Niquille, D.L., Hansen, D.A., Mori, T., Fercher, D., Kries, H., Hilvert, D. Description: Crystal s...

New page

'''Unreleased structure'''

The entry 5n81 is ON HOLD until Paper Publication

Authors: Niquille, D.L., Hansen, D.A., Mori, T., Fercher, D., Kries, H., Hilvert, D.

Description: Crystal structure of an engineered TycA variant in complex with an O-propargyl-beta-Tyr-AMP analog
[[Category: Unreleased Structures]]
[[Category: Fercher, D]]
[[Category: Mori, T]]
[[Category: Hilvert, D]]
[[Category: Kries, H]]
[[Category: Hansen, D.A]]
[[Category: Niquille, D.L]]