8t7j - Revision history

OCA at 16:16, 14 March 2024

OCA — Thu, 14 Mar 2024 16:16:36 GMT

←Older revision		Revision as of 16:16, 14 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/E1CG36_9ACTN E1CG36_9ACTN]		[https://www.uniprot.org/uniprot/E1CG36_9ACTN E1CG36_9ACTN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 A resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family.
-
-	Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15.,Daniel-Ivad PG, Van Lanen S, Ryan KS Biochemistry. 2023 Aug 9. doi: 10.1021/acs.biochem.3c00216. PMID:37556254<ref>PMID:37556254</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8t7j" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:56, 23 August 2023

OCA — Wed, 23 Aug 2023 05:56:49 GMT

←Older revision		Revision as of 05:56, 23 August 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8t7j is ~~ON HOLD until Paper~~ Publication	+	==Oxygen- and PLP-dependent Cap15 holoenzyme bound with phosphate anion==
		+	<StructureSection load='8t7j' size='340' side='right'caption='[[8t7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8t7j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._SANK_62799 Streptomyces sp. SANK 62799]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8T7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8T7J FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=8t7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8t7j OCA], [https://pdbe.org/8t7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8t7j RCSB], [https://www.ebi.ac.uk/pdbsum/8t7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8t7j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E1CG36_9ACTN E1CG36_9ACTN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 A resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family.

-	~~Authors~~:	+	Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15.,Daniel-Ivad PG, Van Lanen S, Ryan KS Biochemistry. 2023 Aug 9. doi: 10.1021/acs.biochem.3c00216. PMID:37556254<ref>PMID:37556254</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8t7j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Streptomyces sp. SANK 62799]]
		+	[[Category: Daniel-Ivad P]]
		+	[[Category: Ryan KS]]

OCA at 11:09, 26 July 2023

OCA — Wed, 26 Jul 2023 11:09:36 GMT

←Older revision		Revision as of 11:09, 26 July 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8t7j is ON HOLD	+	The entry 8t7j is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8t7j" [edit=sysop:move=sysop]

OCA — Wed, 28 Jun 2023 20:06:08 GMT

Protected "8t7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:06, 28 June 2023

OCA: New page: '''Unreleased structure''' The entry 8t7j is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 28 Jun 2023 20:06:07 GMT

New page: '''Unreleased structure''' The entry 8t7j is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8t7j is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]