6y0q - Revision history

OCA at 13:16, 24 January 2024

OCA — Wed, 24 Jan 2024 13:16:43 GMT

←Older revision		Revision as of 13:16, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6y0q' size='340' side='right'caption='[[6y0q]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6y0q' size='340' side='right'caption='[[6y0q]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y0q]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y0q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y0Q 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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=O5W:[(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl]+[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+hydrogen+phosphate'>O5W</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]] 1.75Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jht\|4jht]]</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=O5W:[(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl]+[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+hydrogen+phosphate'>O5W</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0q OCA], [https://pdbe.org/6y0q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0q RCSB], [https://www.ebi.ac.uk/pdbsum/6y0q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0q ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_oxidative_demethylase DNA oxidative demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.33 1.14.11.33] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0q OCA], [~~http~~://pdbe.org/6y0q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y0q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y0q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>	+	[https://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6y0q" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6y0q" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~DNA oxidative demethylase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller, P]]	+	[[Category: Aller P]]
-	[[Category: Axford, D]]	+	[[Category: Axford D]]
-	[[Category: Beale~~, J H~~]]	+	[[Category: Beale JH]]
-	[[Category: Butryn, A]]	+	[[Category: Butryn A]]
-	[[Category: Dirr~~, A S~~]]	+	[[Category: Dirr AS]]
-	[[Category: Kamps~~, J J.A G~~]]	+	[[Category: Kamps JJAG]]
-	[[Category: Lang~~, P A~~]]	+	[[Category: Lang PA]]
-	[[Category: Leissing~~, T M~~]]	+	[[Category: Leissing TM]]
-	[[Category: McDonough~~, M A~~]]	+	[[Category: McDonough MA]]
-	[[Category: Orville~~, A M~~]]	+	[[Category: Orville AM]]
-	[[Category: Owen, R]]	+	[[Category: Owen R]]
-	[[Category: Rabe, P]]	+	[[Category: Rabe P]]
-	[[Category: Schofield~~, C J]]~~	+	[[Category: Schofield CJ]]
-	~~[[Category: 2-oxoglutarate]]~~	+
-	~~[[Category: Dna repair]]~~	+
-	~~[[Category: Iron dependant dioxygenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:46, 30 September 2020

OCA — Wed, 30 Sep 2020 07:46:06 GMT

←Older revision		Revision as of 07:46, 30 September 2020
Line 1:		Line 1:

	==Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA under anaerobic environment using FT-SSX methods==		==Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA under anaerobic environment using FT-SSX methods==
-	<StructureSection load='6y0q' size='340' side='right'caption='[[6y0q]]' scene=''>	+	<StructureSection load='6y0q' size='340' side='right'caption='[[6y0q]], [[Resolution\|resolution]] 1.75Å' 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=6Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y0q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0Q FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0q OCA], [http://pdbe.org/6y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0q RCSB], [http://www.ebi.ac.uk/pdbsum/6y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0q 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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=O5W:[(3~{S},5~{R})-5-(6-azanyl-1-methyl-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl]+[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl+hydrogen+phosphate'>O5W</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4jht\|4jht]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">alkB, aidD, b2212, JW2200 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_oxidative_demethylase DNA oxidative demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.33 1.14.11.33] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0q OCA], [http://pdbe.org/6y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0q RCSB], [http://www.ebi.ac.uk/pdbsum/6y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ALKB_ECOLI ALKB_ECOLI]] Dioxygenase that repairs alkylated DNA and RNA containing 3-methylcytosine or 1-methyladenine by oxidative demethylation. Has highest activity towards 3-methylcytosine. Has lower activity towards alkylated DNA containing ethenoadenine, and no detectable activity towards 1-methylguanine or 3-methylthymine. Accepts double-stranded and single-stranded substrates. Requires molecular oxygen, alpha-ketoglutarate and iron. Provides extensive resistance to alkylating agents such as MMS and DMS (SN2 agents), but not to MMNG and MNU (SN1 agents).<ref>PMID:12226668</ref> <ref>PMID:12594517</ref> <ref>PMID:16482161</ref> <ref>PMID:19706517</ref> <ref>PMID:21068844</ref> <ref>PMID:20084272</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.
		+
		+	Anaerobic fixed-target serial crystallography.,Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374. eCollection, 2020 Sep 1. PMID:32939282<ref>PMID:32939282</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y0q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: DNA oxidative demethylase]]
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller P]]	+	[[Category: Aller, P]]
-	[[Category: Axford D]]	+	[[Category: Axford, D]]
-	[[Category: Beale JH]]	+	[[Category: Beale, J H]]
-	[[Category: Butryn A]]	+	[[Category: Butryn, A]]
-	[[Category: Dirr AS]]	+	[[Category: Dirr, A S]]
-	[[Category: Kamps ~~JJAG~~]]	+	[[Category: Kamps, J J.A G]]
-	[[Category: Lang PA]]	+	[[Category: Lang, P A]]
-	[[Category: Leissing TM]]	+	[[Category: Leissing, T M]]
-	[[Category: McDonough MA]]	+	[[Category: McDonough, M A]]
-	[[Category: Orville AM]]	+	[[Category: Orville, A M]]
-	[[Category: Owen R]]	+	[[Category: Owen, R]]
-	[[Category: Rabe P]]	+	[[Category: Rabe, P]]
-	[[Category: Schofield CJ]]	+	[[Category: Schofield, C J]]
		+	[[Category: 2-oxoglutarate]]
		+	[[Category: Dna repair]]
		+	[[Category: Iron dependant dioxygenase]]
		+	[[Category: Oxidoreductase]]

OCA at 09:34, 9 September 2020

OCA — Wed, 09 Sep 2020 09:34:54 GMT

←Older revision		Revision as of 09:34, 9 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6y0q is ~~ON HOLD until Paper Publication~~	+	==Alpha-ketoglutarate-dependent dioxygenase AlkB in complex with Fe, AKG and methylated DNA under anaerobic environment using FT-SSX methods==
-		+	<StructureSection load='6y0q' size='340' side='right'caption='[[6y0q]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0Q FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6y0q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0q OCA], [http://pdbe.org/6y0q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0q RCSB], [http://www.ebi.ac.uk/pdbsum/6y0q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0q ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Aller P]]
		+	[[Category: Axford D]]
		+	[[Category: Beale JH]]
		+	[[Category: Butryn A]]
		+	[[Category: Dirr AS]]
		+	[[Category: Kamps JJAG]]
		+	[[Category: Lang PA]]
		+	[[Category: Leissing TM]]
		+	[[Category: McDonough MA]]
		+	[[Category: Orville AM]]
		+	[[Category: Owen R]]
		+	[[Category: Rabe P]]
		+	[[Category: Schofield CJ]]

OCA at 04:21, 22 April 2020

OCA — Wed, 22 Apr 2020 04:21:27 GMT

←Older revision		Revision as of 04:21, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y0q is ON HOLD	+	The entry 6y0q is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y0q" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2020 05:25:43 GMT

Protected "6y0q" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:25, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y0q is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Feb 2020 05:25:42 GMT

New page: '''Unreleased structure''' The entry 6y0q is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y0q is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]