6alo - Revision history

OCA at 14:17, 13 March 2024

OCA — Wed, 13 Mar 2024 14:17:40 GMT

←Older revision		Revision as of 14:17, 13 March 2024
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	<StructureSection load='6alo' size='340' side='right'caption='[[6alo]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='6alo' size='340' side='right'caption='[[6alo]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6alo]] 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=6ALO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ALO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6alo]] 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=6ALO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ALO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ARG:ARGININE'>ARG</scene~~>, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OKG:4-peroxy-4-oxobutanoic+acid'>OKG</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]] 1.79Å</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=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OKG:4-peroxy-4-oxobutanoic+acid'>OKG</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=6alo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alo OCA], [https://pdbe.org/6alo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6alo RCSB], [https://www.ebi.ac.uk/pdbsum/6alo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6alo 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=6alo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alo OCA], [~~http~~://pdbe.org/6alo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6alo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6alo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6alo 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;">~~	+
-	~~== 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 6alo" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__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
Line 1:		Line 1:

	==VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and a peroxysuccinate intermediate==		==VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and a peroxysuccinate intermediate==
-	<StructureSection load='6alo' size='340' side='right' caption='[[6alo]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='6alo' size='340' side='right'caption='[[6alo]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6alo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6alo]] 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=6ALO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OKG:4-peroxy-4-oxobutanoic+acid'>OKG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OKG:4-peroxy-4-oxobutanoic+acid'>OKG</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=6alo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alo OCA], [http://pdbe.org/6alo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alo RCSB], [http://www.ebi.ac.uk/pdbsum/6alo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alo 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=6alo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alo OCA], [http://pdbe.org/6alo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alo RCSB], [http://www.ebi.ac.uk/pdbsum/6alo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alo ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6alo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6alo" 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 "6alo" [edit=sysop:move=sysop]

OCA — Wed, 06 Sep 2017 03:50:33 GMT

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

←Older revision

Revision as of 03:50, 6 September 2017

OCA: New page: ==VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and a peroxysuccinate intermediate== == Structural highlights ==
<table><tr><td colspan='2'>[[6alo]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ALO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ALO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OKG:4-peroxy-4-oxobutanoic+acid'>OKG</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=6alo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6alo OCA], [http://pdbe.org/6alo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6alo RCSB], [http://www.ebi.ac.uk/pdbsum/6alo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6alo 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 6alo" 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]]