6y12 - Revision history

OCA at 10:53, 15 November 2023

OCA — Wed, 15 Nov 2023 10:53:37 GMT

←Older revision		Revision as of 10:53, 15 November 2023
Line 3:		Line 3:
	<StructureSection load='6y12' size='340' side='right'caption='[[6y12]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6y12' size='340' side='right'caption='[[6y12]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y12]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~As_4.1305 As 4.1305~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)~~-~~3-HYDROXYARGININE'>ZZU</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]] 1.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6alr\|6alr]]~~, [[~~2wbo~~\|~~2wbo~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~vioC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1960 AS 4.1305]~~)~~</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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [https://pdbe.org/6y12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [https://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 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/Oxidoreductase Oxidoreductase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.14.11.41 1.14.11.41]~~ </~~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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [~~http~~://pdbe.org/6y12 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ARGHX_STRVI ARGHX_STRVI]] Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.<ref>PMID:15368580</ref> <ref>PMID:15368582</ref> <ref>PMID:19490124</ref>	+	[https://www.uniprot.org/uniprot/ARGHX_STRVI ARGHX_STRVI] Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.<ref>PMID:15368580</ref> <ref>PMID:15368582</ref> <ref>PMID:19490124</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 6y12" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6y12" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1305]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Streptomyces vinaceus]]
-	[[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: Arginine hydroxylase]]~~	+
-	~~[[Category: Iron dependent oxygenase~~]]	+

OCA at 07:46, 30 September 2020

OCA — Wed, 30 Sep 2020 07:46:24 GMT

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

	==Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods==		==Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods==
-	<StructureSection load='6y12' size='340' side='right'caption='[[6y12]]' scene=''>	+	<StructureSection load='6y12' size='340' side='right'caption='[[6y12]], [[Resolution\|resolution]] 1.70Å' 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=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1305 As 4.1305]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y12 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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [http://pdbe.org/6y12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [http://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6alr\|6alr]], [[2wbo\|2wbo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vioC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1960 AS 4.1305])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.41 1.14.11.41] </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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [http://pdbe.org/6y12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [http://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ARGHX_STRVI ARGHX_STRVI]] Involved in the biosynthesis of capreomycidine, an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotics such as viomycin and capreomycin. Catalyzes the stereospecific hydroxylation of the C3 of (2S)-arginine to generate (3S)-hydroxy-(2S)-arginine. Usually clavaminic acid synthase-like oxygenases catalyze the formation of threo diastereomers, however VioC produces the erythro diastereomer of beta-carbon-hydroxylated L-arginine. It exerts a broad substrate specificity by accepting the analogs L-homoarginine and L-canavanine for the beta-carbon hydroxylation.<ref>PMID:15368580</ref> <ref>PMID:15368582</ref> <ref>PMID:19490124</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 6y12" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: As 4 1305]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller P]]	+	[[Category: Oxidoreductase]]
-	[[Category: Axford D]]	+	[[Category: Aller, P]]
-	[[Category: Beale JH]]	+	[[Category: Axford, D]]
-	[[Category: Butryn A]]	+	[[Category: Beale, J H]]
-	[[Category: Dirr AS]]	+	[[Category: Butryn, A]]
-	[[Category: Kamps ~~JJAG~~]]	+	[[Category: Dirr, A S]]
-	[[Category: Lang PA]]	+	[[Category: Kamps, J J.A G]]
-	[[Category: Leissing TM]]	+	[[Category: Lang, P A]]
-	[[Category: McDonough MA]]	+	[[Category: Leissing, T M]]
-	[[Category: Orville AM]]	+	[[Category: McDonough, M A]]
-	[[Category: Owen R]]	+	[[Category: Orville, A M]]
-	[[Category: Rabe P]]	+	[[Category: Owen, R]]
-	[[Category: Schofield CJ]]	+	[[Category: Rabe, P]]
		+	[[Category: Schofield, C J]]
		+	[[Category: Arginine hydroxylase]]
		+	[[Category: Iron dependent oxygenase]]

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~~ 6y12 ~~is ON HOLD until Paper Publication~~	+	==Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods==
-		+	<StructureSection load='6y12' size='340' side='right'caption='[[6y12]]' scene=''>
-	~~Authors~~: ~~Rabe, P~~.~~, Beale, J~~.H.~~, Lang, P~~.A.~~, Dirr, A~~.S.~~, Leissing, T~~.M., ~~Butryn, A~~.~~, Aller, P~~.~~, Kamps, J.J.A.G~~., ~~Axford, D~~., ~~McDonough, M~~.A., ~~Orville, A~~.M.~~, Owen, R~~., ~~Schofield, C~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y12 FirstGlance]. <br>
-	~~Description: Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods~~	+	</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=6y12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y12 OCA], [http://pdbe.org/6y12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y12 RCSB], [http://www.ebi.ac.uk/pdbsum/6y12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y12 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Aller, P]]	+	__TOC__
-	[[Category: ~~Rabe, P~~]]	+	</StructureSection>
-	[[Category: ~~Mcdonough, M.A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Beale, J.H~~]]	+	[[Category: Aller P]]
-	[[Category: ~~Kamps, J.J.A.G~~]]	+	[[Category: Axford D]]
-	[[Category: ~~Leissing, T.M~~]]	+	[[Category: Beale JH]]
-	[[Category: ~~Orville, A.M~~]]	+	[[Category: Butryn A]]
-	[[Category: ~~Dirr, A.S~~]]	+	[[Category: Dirr AS]]
-	[[Category: ~~Butryn, A~~]]	+	[[Category: Kamps JJAG]]
-	[[Category: ~~Owen, R~~]]	+	[[Category: Lang PA]]
-	[[Category: ~~Axford, D~~]]	+	[[Category: Leissing TM]]
-	[[Category: ~~Schofield, C.J~~]]	+	[[Category: McDonough MA]]
-	[[Category: ~~Lang, P.A~~]]	+	[[Category: Orville AM]]
		+	[[Category: Owen R]]
		+	[[Category: Rabe P]]
		+	[[Category: Schofield CJ]]

OCA at 04:21, 22 April 2020

OCA — Wed, 22 Apr 2020 04:21:30 GMT

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

-	The entry 6y12 is ON HOLD	+	The entry 6y12 is ON HOLD until Paper Publication

	Authors: Rabe, P., Beale, J.H., Lang, P.A., Dirr, A.S., Leissing, T.M., Butryn, A., Aller, P., Kamps, J.J.A.G., Axford, D., McDonough, M.A., Orville, A.M., Owen, R., Schofield, C.J.		Authors: Rabe, P., Beale, J.H., Lang, P.A., Dirr, A.S., Leissing, T.M., Butryn, A., Aller, P., Kamps, J.J.A.G., Axford, D., McDonough, M.A., Orville, A.M., Owen, R., Schofield, C.J.

-	Description: Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe ~~under anaerobic environment~~ using FT-SSX methods	+	Description: Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen exposure using FT-SSX methods
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Aller, P]]		[[Category: Aller, P]]

OCA: Protected "6y12" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2020 05:26:14 GMT

Protected "6y12" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y12 is ON HOLD Authors: Rabe, P., Beale, J.H., Lang, P.A., Dirr, A.S., Leissing, T.M., Butryn, A., Aller, P., Kamps, J.J.A.G., Axford, D., McDonoug...

OCA — Wed, 19 Feb 2020 05:26:13 GMT

New page: '''Unreleased structure''' The entry 6y12 is ON HOLD Authors: Rabe, P., Beale, J.H., Lang, P.A., Dirr, A.S., Leissing, T.M., Butryn, A., Aller, P., Kamps, J.J.A.G., Axford, D., McDonoug...

New page

'''Unreleased structure'''

The entry 6y12 is ON HOLD

Authors: Rabe, P., Beale, J.H., Lang, P.A., Dirr, A.S., Leissing, T.M., Butryn, A., Aller, P., Kamps, J.J.A.G., Axford, D., McDonough, M.A., Orville, A.M., Owen, R., Schofield, C.J.

Description: Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe under anaerobic environment using FT-SSX methods
[[Category: Unreleased Structures]]
[[Category: Aller, P]]
[[Category: Rabe, P]]
[[Category: Mcdonough, M.A]]
[[Category: Beale, J.H]]
[[Category: Kamps, J.J.A.G]]
[[Category: Leissing, T.M]]
[[Category: Orville, A.M]]
[[Category: Dirr, A.S]]
[[Category: Butryn, A]]
[[Category: Owen, R]]
[[Category: Axford, D]]
[[Category: Schofield, C.J]]
[[Category: Lang, P.A]]