6aln - Revision history

OCA at 10:10, 15 November 2023

OCA — Wed, 15 Nov 2023 10:10:32 GMT

←Older revision		Revision as of 10:10, 15 November 2023
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	<StructureSection load='6aln' size='340' side='right'caption='[[6aln]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6aln' size='340' side='right'caption='[[6aln]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aln]] 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=6ALN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ALN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aln]] 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=6ALN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ALN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AKG:2~~-~~OXOGLUTARIC+ACID'>AKG</scene>~~, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 1.8Å</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='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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6aln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aln OCA], [https://pdbe.org/6aln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6aln RCSB], [https://www.ebi.ac.uk/pdbsum/6aln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6aln 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=6aln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aln OCA], [~~http~~://pdbe.org/6aln PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6aln RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6aln PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6aln 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: As 4 1305]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Streptomyces vinaceus]]
-	[[Category: Boal~~, A K~~]]	+	[[Category: Boal AK]]
-	[[Category: Dunham~~, N P~~]]	+	[[Category: Dunham NP]]
-	[[Category: Mitchell~~, A J]]~~	+	[[Category: Mitchell AJ]]
-	~~[[Category: 2-oxo-glutarate]]~~	+
-	~~[[Category: Hydroxylase]]~~	+
-	~~[[Category: Iron~~]]	+

OCA at 10:03, 1 January 2020

OCA — Wed, 01 Jan 2020 10:03:11 GMT

←Older revision		Revision as of 10:03, 1 January 2020
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	==VioC L-arginine hydroxylase bound to Fe(II), 3S-hydroxy-L-arginine, and 2OG==		==VioC L-arginine hydroxylase bound to Fe(II), 3S-hydroxy-L-arginine, and 2OG==
-	<StructureSection load='6aln' size='340' side='right' caption='[[6aln]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='6aln' size='340' side='right'caption='[[6aln]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6aln]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6aln]] 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=6ALN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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='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='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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6aln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aln OCA], [http://pdbe.org/6aln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aln RCSB], [http://www.ebi.ac.uk/pdbsum/6aln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aln 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=6aln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aln OCA], [http://pdbe.org/6aln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aln RCSB], [http://www.ebi.ac.uk/pdbsum/6aln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aln ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6aln" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6aln" 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: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Boal, A K]]		[[Category: Boal, A K]]

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

OCA — Wed, 06 Sep 2017 03:54:04 GMT

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

←Older revision

Revision as of 03:54, 6 September 2017

OCA: New page: ==VioC L-arginine hydroxylase bound to Fe(II), 3S-hydroxy-L-arginine, and 2OG== == Structural highlights ==
<table><tr><td colspan='2'>[[6aln]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALN FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=ZZU:(2S,3S)-3-HYDROXYARGININE'>ZZU</scene></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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6aln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6aln OCA], [http://pdbe.org/6aln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6aln RCSB], [http://www.ebi.ac.uk/pdbsum/6aln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6aln ProSAT]</span></td></tr>
</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 ==
Iron(II)- and 2-(oxo)-glutarate-dependent oxygenases catalyze diverse oxidative transformations that are often initiated by abstraction of hydrogen from carbon by iron(IV)-oxo (ferryl) complexes. Control of the relative orientation of the substrate C-H and ferryl Fe-O bonds, primarily by direction of the oxo group into one of two cis-related coordination sites (termed inline and offline), may be generally important for control of the reaction outcome. Neither the ferryl complexes nor their fleeting precursors have been crystallographically characterized, hindering direct experimental validation of the offline hypothesis and elucidation of the means by which the protein might dictate an alternative oxo position. Comparison of high-resolution x-ray crystal structures of the substrate complex, an Fe(II)-peroxysuccinate ferryl precursor, and a vanadium(IV)-oxo mimic of the ferryl intermediate in the L-arginine 3-hydroxylase, VioC, reveals coordinated motions of active site residues that appear to control the intermediate geometries to determine reaction outcome.

Visualizing the reaction cycle in an iron(II)- and 2-(oxo)-glutarate-dependent hydroxylase.,Mitchell AJ, Dunham NP, Martinie RJ, Bergman JA, Pollock CJ, Hu K, Allen BD, Chang WC, Silakov A, Bollinger JM Jr, Krebs C, Boal AK J Am Chem Soc. 2017 Aug 20. doi: 10.1021/jacs.7b07374. PMID:28823155<ref>PMID:28823155</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6aln" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Oxidoreductase]]
[[Category: Boal, A K]]
[[Category: Dunham, N P]]
[[Category: Mitchell, A J]]
[[Category: 2-oxo-glutarate]]
[[Category: Hydroxylase]]
[[Category: Iron]]