6db2 - Revision history

OCA at 14:33, 13 March 2024

OCA — Wed, 13 Mar 2024 14:33:31 GMT

←Older revision		Revision as of 14:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6db2' size='340' side='right'caption='[[6db2]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6db2' size='340' side='right'caption='[[6db2]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6db2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6db2]] 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=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</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='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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</scene></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=6db2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db2 OCA], [~~http~~://pdbe.org/6db2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6db2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6db2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6db2 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=6db2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db2 OCA], [https://pdbe.org/6db2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6db2 RCSB], [https://www.ebi.ac.uk/pdbsum/6db2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6db2 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 ==~~	+
-	Hydroxylation of aliphatic carbons by non-heme Fe(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe(III)-coordinated oxygen (termed rebound). Enzymes that use H-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C-C desaturations, it has been proposed that a second HAT to the Fe(III)-OH complex from the carbon alpha to the radical preempts rebound. Deuterium ((2)H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related L-arginine-modifying iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the L-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H* first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors (1)H or (2)H. By contrast, an unexpected 3,4-desaturation of L-homoarginine (L-hArg) by VioC, the L-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors (2)H. Anchimeric assistance by N6 permits removal of the C4-H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (</= 3.5 A) of both L-hArg carbons to the (hydr)oxo group in an x-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may ensure competing hydroxylation, thus explaining why nearly all natural substrates for Fe/2OG desaturases have alpha-heteroatoms.	+
-		+
-	Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance.,Dunham NP, Chang WC, Mitchell AJ, Martinie RJ, Zhang B, Bergman JA, Rajakovich LJ, Wang B, Silakov A, Krebs C, Boal AK, Bollinger JM Jr J Am Chem Soc. 2018 Apr 30. doi: 10.1021/jacs.8b01933. PMID:29708749<ref>PMID:29708749</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6db2" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 18:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Oxidoreductase]]
	[[Category: Streptomyces vinaceus]]		[[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: Desaturase]]~~	+
-	~~[[Category: Desaturation]]~~	+
-	~~[[Category: Hydroxylase]]~~	+
-	~~[[Category: Hydroxylation]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Oxygenase]]~~	+
-	~~[[Category: Viomycin~~]]	+

OCA at 10:58, 1 January 2020

OCA — Wed, 01 Jan 2020 10:58:11 GMT

←Older revision		Revision as of 10:58, 1 January 2020
Line 1:		Line 1:

	==X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate==		==X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate==
-	<StructureSection load='6db2' size='340' side='right' caption='[[6db2]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='6db2' size='340' side='right'caption='[[6db2]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6db2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6db2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6db2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6db2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Hydroxylases 3D structures\|Hydroxylases 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Streptomyces vinaceus]]		[[Category: Streptomyces vinaceus]]

OCA at 05:34, 16 May 2018

OCA — Wed, 16 May 2018 05:34:01 GMT

←Older revision		Revision as of 05:34, 16 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6db2 is ~~ON HOLD~~	+	==X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate==
		+	<StructureSection load='6db2' size='340' side='right' caption='[[6db2]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6db2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_vinaceus Streptomyces vinaceus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HRG:L-HOMOARGININE'>HRG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=VVO:oxovanadium(2+)'>VVO</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=6db2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db2 OCA], [http://pdbe.org/6db2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db2 RCSB], [http://www.ebi.ac.uk/pdbsum/6db2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db2 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 ==
		+	Hydroxylation of aliphatic carbons by non-heme Fe(IV)-oxo (ferryl) complexes proceeds by hydrogen-atom (H) transfer (HAT) to the ferryl and subsequent coupling between the carbon radical and Fe(III)-coordinated oxygen (termed rebound). Enzymes that use H-abstracting ferryl complexes for other transformations must either suppress rebound or further process hydroxylated intermediates. For olefin-installing C-C desaturations, it has been proposed that a second HAT to the Fe(III)-OH complex from the carbon alpha to the radical preempts rebound. Deuterium ((2)H) at the second site should slow this step, potentially making rebound competitive. Desaturations mediated by two related L-arginine-modifying iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases behave oppositely in this key test, implicating different mechanisms. NapI, the L-Arg 4,5-desaturase from the naphthyridinomycin biosynthetic pathway, abstracts H* first from C5 but hydroxylates this site (leading to guanidine release) to the same modest extent whether C4 harbors (1)H or (2)H. By contrast, an unexpected 3,4-desaturation of L-homoarginine (L-hArg) by VioC, the L-Arg 3-hydroxylase from the viomycin biosynthetic pathway, is markedly disfavored relative to C4 hydroxylation when C3 (the second hydrogen donor) harbors (2)H. Anchimeric assistance by N6 permits removal of the C4-H as a proton in the NapI reaction, but, with no such assistance possible in the VioC desaturation, a second HAT step (from C3) is required. The close proximity (</= 3.5 A) of both L-hArg carbons to the (hydr)oxo group in an x-ray crystal structure of VioC harboring a vanadium-based ferryl mimic supports and rationalizes the sequential-HAT mechanism. The results suggest that, although the sequential-HAT mechanism is feasible, its geometric requirements may ensure competing hydroxylation, thus explaining why nearly all natural substrates for Fe/2OG desaturases have alpha-heteroatoms.

-	~~Authors~~: Dunham, ~~N.P.~~, Mitchell, A~~.J.~~, Boal, A.K.	+	Two Distinct Mechanisms for C-C Desaturation by Iron(II)- and 2-(Oxo)glutarate-Dependent Oxygenases: Importance of alpha-Heteroatom Assistance.,Dunham NP, Chang WC, Mitchell AJ, Martinie RJ, Zhang B, Bergman JA, Rajakovich LJ, Wang B, Silakov A, Krebs C, Boal AK, Bollinger JM Jr J Am Chem Soc. 2018 Apr 30. doi: 10.1021/jacs.8b01933. PMID:29708749<ref>PMID:29708749</ref>

-	~~Description: X-ray crystal structure of VioC bound to vanadyl ion~~, L-~~homoarginine, and succinate~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Boal, A.K]]	+	<div class="pdbe-citations 6db2" style="background-color:#fffaf0;"></div>
-	[[Category: Mitchell, A.J]]	+	== References ==
-	[[Category: ~~Dunham, N.P~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oxidoreductase]]
		+	[[Category: Streptomyces vinaceus]]
		+	[[Category: Boal, A K]]
		+	[[Category: Dunham, N P]]
		+	[[Category: Mitchell, A J]]
		+	[[Category: Desaturase]]
		+	[[Category: Desaturation]]
		+	[[Category: Hydroxylase]]
		+	[[Category: Hydroxylation]]
		+	[[Category: Metalloenzyme]]
		+	[[Category: Oxygenase]]
		+	[[Category: Viomycin]]

OCA: Protected "6db2" [edit=sysop:move=sysop]

OCA — Wed, 09 May 2018 04:57:07 GMT

Protected "6db2" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:57, 9 May 2018

OCA: New page: '''Unreleased structure''' The entry 6db2 is ON HOLD Authors: Dunham, N.P., Mitchell, A.J., Boal, A.K. Description: X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine...

OCA — Wed, 09 May 2018 04:57:06 GMT

New page: '''Unreleased structure''' The entry 6db2 is ON HOLD Authors: Dunham, N.P., Mitchell, A.J., Boal, A.K. Description: X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine...

New page

'''Unreleased structure'''

The entry 6db2 is ON HOLD

Authors: Dunham, N.P., Mitchell, A.J., Boal, A.K.

Description: X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, and succinate
[[Category: Unreleased Structures]]
[[Category: Boal, A.K]]
[[Category: Mitchell, A.J]]
[[Category: Dunham, N.P]]