7w5t - Revision history

OCA at 17:36, 29 November 2023

OCA — Wed, 29 Nov 2023 17:36:37 GMT

←Older revision		Revision as of 17:36, 29 November 2023
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	<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]], [[Resolution\|resolution]] 1.74Å' scene=''>		<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7w5t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7w5t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinomadura_sp._ATCC_39365 Actinomadura sp. ATCC 39365]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.74Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t 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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1U8X168_9ACTN A0A1U8X168_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Actinomadura sp. ATCC 39365]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Dai~~, L H~~]]	+	[[Category: Dai LH]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Hu~~, Y M~~]]	+	[[Category: Hu YM]]
-	[[Category: Huang~~, J W~~]]	+	[[Category: Huang JW]]
-	[[Category: Zhang, X]]	+	[[Category: Zhang X]]
-	~~[[Category: Halogenase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 13:10, 4 May 2022

OCA — Wed, 04 May 2022 13:10:35 GMT

←Older revision		Revision as of 13:10, 4 May 2022
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	==A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates==		==A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates==
-	<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]]' scene=''>	+	<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]], [[Resolution\|resolution]] 1.74Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7w5t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br>
-	</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenases (NHFeHals), which catalyze the regio- and stereoselective halogenation of the unactivated C(sp(3))-H bonds, exhibit tremendous potential in the challenging asymmetric halogenation. AdeV from Actinomadura sp. ATCC 39365 is the first identified carrier protein-free NHFeHal that catalyzes the chlorination of nucleotide 2'-deoxyadenosine-5'-monophosphate (2'-dAMP) to afford 2'-chloro-2'-deoxyadenosine-5'-monophosphate. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG at resolutions of 1.76 and 1.74 A, respectively. AdeV possesses a typical beta-sandwich topology with H194, H252, alphaKG, chloride, and one water molecule coordinating Fe(II) in the active site. Molecular docking, mutagenesis, and biochemical analyses reveal that the hydrophobic interactions and hydrogen bond network between the substrate-binding pocket and the adenine, deoxyribose, and phosphate moieties of 2'-dAMP are essential for substrate recognition. Residues H111, R177, and H192 might play important roles in the second-sphere interactions that control reaction partitioning. This study provides valuable insights into the catalytic selectivity of AdeV and will facilitate the rational engineering of AdeV and other NHFeHals for synthesis of halogenated nucleotides. IMPORTANCE Halogenated nucleotides are a group of important antibiotics and are clinically used as antiviral and anticancer drugs. AdeV is the first carrier protein-independent nonheme iron- and alpha-ketoglutarate (alphaKG)-dependent halogenase (NHFeHal) that can selectively halogenate nucleotides and exhibits restricted substrate specificity toward several 2'-dAMP analogues. Here, we determined the complex crystal structures of AdeV/Fe(II)/Cl and AdeV/Fe(II)/Cl/alphaKG. Molecular docking, mutagenesis, and biochemical analyses provide important insights into the catalytic selectivity of AdeV. This study will facilitate the rational engineering of AdeV and other carrier protein-independent NHFeHals for synthesis of halogenated nucleotides.
		+
		+	Structural and Functional Insights into a Nonheme Iron- and alpha-Ketoglutarate-Dependent Halogenase That Catalyzes Chlorination of Nucleotide Substrates.,Dai L, Zhang X, Hu Y, Shen J, Zhang Q, Zhang L, Min J, Chen CC, Liu Y, Huang JW, Guo RT Appl Environ Microbiol. 2022 Apr 18:e0249721. doi: 10.1128/aem.02497-21. PMID:35435717<ref>PMID:35435717</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7w5t" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen CC]]	+	[[Category: Chen, C C]]
-	[[Category: Dai LH]]	+	[[Category: Dai, L H]]
-	[[Category: Guo RT]]	+	[[Category: Guo, R T]]
-	[[Category: Hu YM]]	+	[[Category: Hu, Y M]]
-	[[Category: Huang JW]]	+	[[Category: Huang, J W]]
-	[[Category: Zhang X]]	+	[[Category: Zhang, X]]
		+	[[Category: Halogenase]]
		+	[[Category: Transferase]]

OCA at 09:49, 13 April 2022

OCA — Wed, 13 Apr 2022 09:49:18 GMT

←Older revision		Revision as of 09:49, 13 April 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7w5t is ~~ON HOLD until Paper Publication~~	+	==A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates==
-		+	<StructureSection load='7w5t' size='340' side='right'caption='[[7w5t]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W5T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W5T FirstGlance]. <br>
-	~~Description~~:	+	</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=7w5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w5t OCA], [https://pdbe.org/7w5t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w5t RCSB], [https://www.ebi.ac.uk/pdbsum/7w5t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w5t ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen CC]]
		+	[[Category: Dai LH]]
		+	[[Category: Guo RT]]
		+	[[Category: Hu YM]]
		+	[[Category: Huang JW]]
		+	[[Category: Zhang X]]

OCA at 08:42, 12 January 2022

OCA — Wed, 12 Jan 2022 08:42:26 GMT

←Older revision		Revision as of 08:42, 12 January 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7w5t is ON HOLD	+	The entry 7w5t is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7w5t" [edit=sysop:move=sysop]

OCA — Wed, 08 Dec 2021 08:46:09 GMT

Protected "7w5t" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:46, 8 December 2021

OCA: New page: '''Unreleased structure''' The entry 7w5t is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 08 Dec 2021 08:46:08 GMT

New page: '''Unreleased structure''' The entry 7w5t is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7w5t is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]