5kag - Revision history

OCA at 09:57, 27 September 2023

OCA — Wed, 27 Sep 2023 09:57:12 GMT

←Older revision		Revision as of 09:57, 27 September 2023
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	<StructureSection load='5kag' size='340' side='right'caption='[[5kag]], [[Resolution\|resolution]] 2.46Å' scene=''>		<StructureSection load='5kag' size='340' side='right'caption='[[5kag]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kag]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_toyocaensis"_nishimura_et_al. "streptomyces~~ toyocaensis~~" nishimura et al.~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KAG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kag]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KAG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</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]] 2.456Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]], [[5kaj\|5kaj]], [[5kah\|5kah]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BU52_01220 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 "Streptomyces toyocaensis" Nishimura et al.])</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=5kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kag OCA], [https://pdbe.org/5kag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kag RCSB], [https://www.ebi.ac.uk/pdbsum/5kag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kag 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=1.13.11.80 1.13.11.80] </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=5kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kag OCA], [~~http~~://pdbe.org/5kag PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kag RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kag PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kag ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO]] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</ref>	+	[https://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</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: Streptomyces toyocaensis nishimura et al]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Streptomyces toyocaensis]]
-	[[Category: Bruner~~, S D~~]]	+	[[Category: Bruner SD]]
-	[[Category: Condurso~~, H L~~]]	+	[[Category: Condurso HL]]
-	[[Category: Fielding~~, E N~~]]	+	[[Category: Fielding EN]]
-	[[Category: Li, K]]	+	[[Category: Li K]]
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Dpgc~~]]	+

OCA at 12:09, 25 December 2019

OCA — Wed, 25 Dec 2019 12:09:36 GMT

←Older revision		Revision as of 12:09, 25 December 2019
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	==Crystal structure of a dioxygenase in the Crotonase superfamily in P21==		==Crystal structure of a dioxygenase in the Crotonase superfamily in P21==
-	<StructureSection load='5kag' size='340' side='right' caption='[[5kag]], [[Resolution\|resolution]] 2.46Å' scene=''>	+	<StructureSection load='5kag' size='340' side='right'caption='[[5kag]], [[Resolution\|resolution]] 2.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5kag]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_toyocaensis"_nishimura_et_al. "streptomyces toyocaensis" nishimura et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KAG FirstGlance]. <br>		<table><tr><td colspan='2'>[[5kag]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_toyocaensis"_nishimura_et_al. "streptomyces toyocaensis" nishimura et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KAG FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Streptomyces toyocaensis nishimura et al]]		[[Category: Streptomyces toyocaensis nishimura et al]]
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Bruner, S D]]		[[Category: Bruner, S D]]

OCA at 05:56, 16 November 2017

OCA — Thu, 16 Nov 2017 05:56:57 GMT

←Older revision		Revision as of 05:56, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kag is ~~ON HOLD~~	+	==Crystal structure of a dioxygenase in the Crotonase superfamily in P21==
		+	<StructureSection load='5kag' size='340' side='right' caption='[[5kag]], [[Resolution\|resolution]] 2.46Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kag]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_toyocaensis"_nishimura_et_al. "streptomyces toyocaensis" nishimura et al.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KAG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KAG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]], [[5kaj\|5kaj]], [[5kah\|5kah]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BU52_01220 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 "Streptomyces toyocaensis" Nishimura et al.])</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=1.13.11.80 1.13.11.80] </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=5kag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kag OCA], [http://pdbe.org/5kag PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kag RCSB], [http://www.ebi.ac.uk/pdbsum/5kag PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kag ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO]] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The enzyme DpgC is included in the small family of cofactor-independent dioxygenases. The chemistry of DpgC is uncommon as the protein binds and utilizes dioxygen without the aid of a metal or organic cofactor. Previous structural and biochemical studies identified the substrate-binding mode and the components of the active site that are important in the catalytic mechanism. In addition, the results delineated a putative binding pocket and migration pathway for the co-substrate dioxygen. Here, structural biology is utilized, along with site-directed mutagenesis, to probe the assigned dioxygen-binding pocket. The key residues implicated in dioxygen trafficking were studied to probe the process of binding, activation and chemistry. The results support the proposed chemistry and provide insight into the general mechanism of dioxygen binding and activation.

-	~~Authors: Li~~, K., Fielding~~, E.N.~~, Condurso, H.L., ~~Bruner, S~~.D.	+	Probing the structural basis of oxygen binding in a cofactor-independent dioxygenase.,Li K, Fielding EN, Condurso HL, Bruner SD Acta Crystallogr D Struct Biol. 2017 Jul 1;73(Pt 7):573-580. doi:, 10.1107/S2059798317007045. Epub 2017 Jun 30. PMID:28695857<ref>PMID:28695857</ref>

-	~~Description: Crystal structure of~~ a ~~dioxygenase in~~ the ~~Crotonase superfamily in P21~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kag" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Streptomyces toyocaensis nishimura et al]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Bruner, S D]]
		+	[[Category: Condurso, H L]]
		+	[[Category: Fielding, E N]]
	[[Category: Li, K]]		[[Category: Li, K]]
-	[[Category: ~~Condurso, H.L~~]]	+	[[Category: Dioxygenase]]
-	[[Category: ~~Bruner, S.D]]~~	+	[[Category: Dpgc]]
-	~~[[Category: Fielding, E.N~~]]	+

OCA at 10:13, 9 March 2017

OCA — Thu, 09 Mar 2017 10:13:46 GMT

←Older revision		Revision as of 10:13, 9 March 2017
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	[[Category: Li, K]]		[[Category: Li, K]]
	[[Category: Condurso, H.L]]		[[Category: Condurso, H.L]]
-	[[Category: Fielding, E.N]]
	[[Category: Bruner, S.D]]		[[Category: Bruner, S.D]]
		+	[[Category: Fielding, E.N]]

OCA: Protected "5kag" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 13:38:16 GMT

Protected "5kag" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:38, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kag is ON HOLD Authors: Li, K., Fielding, E.N., Condurso, H.L., Bruner, S.D. Description: Crystal structure of a dioxygenase in the Crotonase supe...

OCA — Mon, 20 Jun 2016 13:38:14 GMT

New page: '''Unreleased structure''' The entry 5kag is ON HOLD Authors: Li, K., Fielding, E.N., Condurso, H.L., Bruner, S.D. Description: Crystal structure of a dioxygenase in the Crotonase supe...

New page

'''Unreleased structure'''

The entry 5kag is ON HOLD

Authors: Li, K., Fielding, E.N., Condurso, H.L., Bruner, S.D.

Description: Crystal structure of a dioxygenase in the Crotonase superfamily in P21
[[Category: Unreleased Structures]]
[[Category: Li, K]]
[[Category: Condurso, H.L]]
[[Category: Fielding, E.N]]
[[Category: Bruner, S.D]]