5tu4 - Revision history

OCA at 14:23, 6 March 2024

OCA — Wed, 06 Mar 2024 14:23:13 GMT

←Older revision		Revision as of 14:23, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5tu4' size='340' side='right'caption='[[5tu4]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5tu4' size='340' side='right'caption='[[5tu4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tu4]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Planktothrix_agardhii_nies~~-596 Planktothrix agardhii ~~nies~~-596]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tu4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Planktothrix_agardhii_NIES-596 Planktothrix agardhii NIES-596]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TU4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1C:N-(TERT-BUTOXYCARBONYL)-L-TYROSINE'>B1C</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tyy\|5tyy]], [[5tu5\|5tu5]], [[5tu6\|5tu6]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B1C:N-(TERT-BUTOXYCARBONYL)-L-TYROSINE'>B1C</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pagF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=443922 Planktothrix agardhii NIES-596])</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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [https://pdbe.org/5tu4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [https://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [~~http~~://pdbe.org/5tu4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/F5B6Z0_PLAAG F5B6Z0_PLAAG]
-	The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. Unexpectedly, the structures reveal a truncated barrel fold, wherein binding of large peptide substrates is necessary to complete a solvent-exposed hydrophobic pocket to form the catalytically competent active site. Kinetic, mutational, chemical, and computational analyses revealed the structural basis of selectivity, showing a small motif within peptide substrates that is sufficient for recognition by the enzyme. Attaching this 2-residue motif to two random peptides results in their isoprenylation by PagF, demonstrating utility as a general biocatalytic platform for modifications on any peptide substrate.	+
-		+
-	Molecular basis for the broad substrate selectivity of a peptide prenyltransferase.,Hao Y, Pierce E, Roe D, Morita M, McIntosh JA, Agarwal V, Cheatham TE 3rd, Schmidt EW, Nair SK Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):~~14037-14042. Epub 2016 Nov 21. PMID:27872314<ref>PMID:27872314<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 5tu4" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Planktothrix agardhii ~~nies~~-596]]	+	[[Category: Planktothrix agardhii NIES-596]]
-	[[Category: Hao, Y]]	+	[[Category: Hao Y]]
-	[[Category: Nair~~, S K]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Abba fold]]~~	+
-	~~[[Category: Prenylation]]~~	+
-	~~[[Category: Ripp]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:56, 2 October 2019

OCA — Wed, 02 Oct 2019 10:56:33 GMT

←Older revision		Revision as of 10:56, 2 October 2019
Line 1:		Line 1:

	==PagF with Boc-Tyr and DMSPP==		==PagF with Boc-Tyr and DMSPP==
-	<StructureSection load='5tu4' size='340' side='right' caption='[[5tu4]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5tu4' size='340' side='right'caption='[[5tu4]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tu4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tu4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Planktothrix_agardhii_nies-596 Planktothrix agardhii nies-596]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1C:N-(TERT-BUTOXYCARBONYL)-L-TYROSINE'>B1C</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <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=B1C:N-(TERT-BUTOXYCARBONYL)-L-TYROSINE'>B1C</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <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">[[5tyy\|5tyy]], [[5tu5\|5tu5]], [[5tu6\|5tu6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5tyy\|5tyy]], [[5tu5\|5tu5]], [[5tu6\|5tu6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pagF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=443922 Planktothrix agardhii NIES-596])</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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [http://pdbe.org/5tu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [http://pdbe.org/5tu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Planktothrix agardhii nies-596]]
	[[Category: Hao, Y]]		[[Category: Hao, Y]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]

OCA at 14:45, 22 December 2016

OCA — Thu, 22 Dec 2016 14:45:38 GMT

←Older revision		Revision as of 14:45, 22 December 2016
Line 8:		Line 8:
	<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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [http://pdbe.org/5tu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 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=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [http://pdbe.org/5tu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The cyanobactin prenyltransferases catalyze a series of known or unprecedented reactions on millions of different substrates, with no easily observable recognition motif and exquisite regioselectivity. Here we define the basis of broad substrate tolerance for the otherwise uncharacterized TruF family. We determined the structures of the Tyr-prenylating enzyme PagF, in complex with an isoprenoid donor analog and a panel of linear and macrocyclic peptide substrates. Unexpectedly, the structures reveal a truncated barrel fold, wherein binding of large peptide substrates is necessary to complete a solvent-exposed hydrophobic pocket to form the catalytically competent active site. Kinetic, mutational, chemical, and computational analyses revealed the structural basis of selectivity, showing a small motif within peptide substrates that is sufficient for recognition by the enzyme. Attaching this 2-residue motif to two random peptides results in their isoprenylation by PagF, demonstrating utility as a general biocatalytic platform for modifications on any peptide substrate.
		+
		+	Molecular basis for the broad substrate selectivity of a peptide prenyltransferase.,Hao Y, Pierce E, Roe D, Morita M, McIntosh JA, Agarwal V, Cheatham TE 3rd, Schmidt EW, Nair SK Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14037-14042. Epub 2016 Nov 21. PMID:27872314<ref>PMID:27872314</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5tu4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA: Protected "5tu4" [edit=sysop:move=sysop]

OCA — Sat, 10 Dec 2016 18:39:34 GMT

Protected "5tu4" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:39, 10 December 2016

OCA: New page: ==PagF with Boc-Tyr and DMSPP== == Structural highlights ==
OCA — Sat, 10 Dec 2016 18:39:32 GMT

New page: ==PagF with Boc-Tyr and DMSPP== <StructureSection load='5tu4' size='340' side='right' caption='5tu4, resolution 2.10Å' scene=''> == Structural highlights == <tabl...

New page

==PagF with Boc-Tyr and DMSPP==
<StructureSection load='5tu4' size='340' side='right' caption='[[5tu4]], [[Resolution|resolution]] 2.10Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5tu4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TU4 OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TU4 FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=B1C:N-(TERT-BUTOXYCARBONYL)-L-TYROSINE'>B1C</scene>, <scene name='pdbligand=DST:DIMETHYLALLYL+S-THIOLODIPHOSPHATE'>DST</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5tyy|5tyy]], [[5tu5|5tu5]], [[5tu6|5tu6]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5tu4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tu4 OCA], [http://pdbe.org/5tu4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tu4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tu4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tu4 ProSAT]</td></tr>
</table>
TOC
</StructureSection>
[[Category: Hao, Y]]
[[Category: Nair, S K]]
[[Category: Abba fold]]
[[Category: Prenylation]]
[[Category: Ripp]]
[[Category: Transferase]]