2pg8 - Revision history

OCA at 11:01, 30 August 2023

2023-08-30T11:01:20Z

← Older revision		Revision as of 11:01, 30 August 2023
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	<StructureSection load='2pg8' size='340' side='right'caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2pg8' size='340' side='right'caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [https://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=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pg8]] is a 3 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=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>
	</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>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2np9\|2np9]]</div></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">DpgC ([https://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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [https://pdbe.org/2pg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pg8 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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [https://pdbe.org/2pg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pg8 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[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>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Streptomyces toyocaensis nishimura et al]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Fielding, E N~~]]		[[Category: Streptomyces toyocaensis]]
	[[Category: ~~Ligand binding protein]]~~		[[Category: Fielding EN]]
	~~[[Category: Protein-ligand complex~~]]

OCA at 15:23, 17 June 2021

2021-06-17T15:23:24Z

← Older revision		Revision as of 15:23, 17 June 2021
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	==Crystal structure of R254K mutanat of DpgC with bound substrate analog==		==Crystal structure of R254K mutanat of DpgC with bound substrate analog==
	<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2pg8' size='340' side='right'caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pg8]] is a 3 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=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [https://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=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PG8 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2np9\|2np9]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([~~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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [~~http~~://pdbe.org/2pg8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pg8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pg8 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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [https://pdbe.org/2pg8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [https://www.ebi.ac.uk/pdbsum/2pg8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pg8_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pg8_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</StructureSection>		</StructureSection>
	[[Category: Streptomyces toyocaensis nishimura et al]]		[[Category: Streptomyces toyocaensis nishimura et al]]
			[[Category: Large Structures]]
	[[Category: Fielding, E N]]		[[Category: Fielding, E N]]
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 09:25, 18 October 2017

2017-10-18T09:25:01Z

← Older revision		Revision as of 09:25, 18 October 2017
Line 1:		Line 1:

	==Crystal structure of R254K mutanat of DpgC with bound substrate analog==		==Crystal structure of R254K mutanat of DpgC with bound substrate analog==
	<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://pdbe.org/2pg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://pdbe.org/2pg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pg8 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2pg8 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:43, 11 September 2015

2015-09-11T11:43:06Z

← Older revision		Revision as of 11:43, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_toyocaensis Streptomyces~~ toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pg8]] is a 3 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=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 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='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]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://pdbe.org/2pg8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2pg8" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces toyocaensis]]		[[Category: Streptomyces toyocaensis nishimura et al]]
	[[Category: Fielding, E N]]		[[Category: Fielding, E N]]
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 15:59, 19 January 2015

2015-01-19T15:59:37Z

← Older revision		Revision as of 15:59, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>
	</td></tr><tr><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><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</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=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Streptomyces toyocaensis]]		[[Category: Streptomyces toyocaensis]]
	[[Category: Fielding, E N.]]		[[Category: Fielding, E N]]
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA at 19:04, 30 September 2014

2014-09-30T19:04:47Z

← Older revision		Revision as of 19:04, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2pg8~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of R254K mutanat of DpgC with bound substrate analog==
			<StructureSection load='2pg8' size='340' side='right' caption='[[2pg8]], [[Resolution\|resolution]] 3.00Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PG8 FirstGlance]. <br>
			</td></tr><tr><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><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2np9\|2np9]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pg8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pg8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pg8 RCSB], [http://www.ebi.ac.uk/pdbsum/2pg8 PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pg8_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The enzyme DpgC belongs to a small class of oxygenases not dependent on accessory cofactors for activity. DpgC is in the biosynthetic pathway for the nonproteinogenic amino acid 3,5-dihydroxyphenylglycine in actinomycetes bacteria responsible for the production of the vancomycin/teicoplanin family of antibiotic natural products. The X-ray structure of DpgC [Widboom, P. W., Fielding, E. N., Liu, Y., and Bruner, S. D. (2007) Nature 447, 342-345] confirmed the absence of cofactors and defined a novel hydrophobic dioxygen binding pocket adjacent to a bound substrate analogue. In this paper, the role specific amino acids play in substrate recognition and catalysis is examined through biochemical and structural characterization of site-specific enzyme mutations and alternate substrates. The results establish the importance of three amino acids, Arg254, Glu299, and Glu189, in the chemistry of DpgC. Arg254 and Glu189 join to form a specific contact with one of the phenolic hydroxyls of the substrate, and this interaction plays a key role in both substrate recognition and catalysis. The X-ray crystal structure of Arg254Lys was determined to address the role this residue plays in the chemistry. In addition, characterization of alternate substrate analogues demonstrates the presence and position of phenol groups are necessary for both enzyme recognition and downstream oxidation chemistry. Overall, this work defines the mechanism of substrate recognition and specificity by the cofactor-independent dioxygenase DpgC.

	~~{{STRUCTURE_2pg8\| PDB=2pg8 \| SCENE= }}~~		Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC.,Fielding EN, Widboom PF, Bruner SD Biochemistry. 2007 Dec 11;46(49):13994-4000. Epub 2007 Nov 16. PMID:18004875<ref>PMID:18004875</ref>

	~~===Crystal structure of R254K mutanat~~ of ~~DpgC with bound substrate analog===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18004875}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2pg8]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018004875<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Streptomyces toyocaensis]]		[[Category: Streptomyces toyocaensis]]
	[[Category: Fielding, E N.]]		[[Category: Fielding, E N.]]
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

OCA: Protected "2pg8" [edit=sysop:move=sysop]

2013-01-07T11:23:04Z

Protected "2pg8" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:23, 7 January 2013
(No difference)

OCA at 11:23, 7 January 2013

2013-01-07T11:23:01Z

← Older revision		Revision as of 11:23, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2pg8.png\|left\|200px]]		[[Image:2pg8.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2pg8", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2pg8\| PDB=2pg8 \| SCENE= }}		{{STRUCTURE_2pg8\| PDB=2pg8 \| SCENE= }}

	===Crystal structure of R254K mutanat of DpgC with bound substrate analog===		===Crystal structure of R254K mutanat of DpgC with bound substrate analog===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18004875}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18004875 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18004875}}		{{ABSTRACT_PUBMED_18004875}}

	==About this Structure==		==About this Structure==
	~~2PG8~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].		[[2pg8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18004875~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018004875</ref><references group="xtra"/>
	[[Category: Streptomyces toyocaensis]]		[[Category: Streptomyces toyocaensis]]
	[[Category: Fielding, E N.]]		[[Category: Fielding, E N.]]
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:08:19 2009''~~

OCA at 19:08, 17 February 2009

2009-02-17T19:08:20Z

← Older revision		Revision as of 19:08, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2PG8 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].		2PG8 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PG8 OCA].

	==Reference==		==Reference==
	~~Substrate recognition and catalysis by the cofactor-independent dioxygenase DpgC., Fielding EN, Widboom PF, Bruner SD, Biochemistry. 2007 Dec 11;46(49):13994-4000. Epub 2007 Nov 16.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18004875 18004875]~~		<ref group="xtra">PMID:18004875</ref><references group="xtra"/>
	~~[[Category: Single protein]]~~
	[[Category: Streptomyces toyocaensis]]		[[Category: Streptomyces toyocaensis]]
	[[Category: Fielding, E N.]]		[[Category: Fielding, E N.]]
Line 30:		Line 29:
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 05~~:11:~~31 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 21:08:19 2009''

OCA at 02:11, 29 July 2008

2008-07-29T02:11:33Z

← Older revision		Revision as of 02:11, 29 July 2008
Line 1:		Line 1:
	[[Image:2pg8.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:2pg8.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2pg8\| PDB=2pg8 \| SCENE= }}		{{STRUCTURE_2pg8\| PDB=2pg8 \| SCENE= }}

	~~'''~~Crystal structure of R254K mutanat of DpgC with bound substrate analog~~'''~~		===Crystal structure of R254K mutanat of DpgC with bound substrate analog===


	~~==Overview==~~		<!--
	The ~~enzyme DpgC belongs to a small class of oxygenases not dependent on accessory cofactors for activity. DpgC is in the biosynthetic pathway for the nonproteinogenic amino acid 3~~,~~5-dihydroxyphenylglycine in actinomycetes bacteria responsible for~~ the ~~production of~~ the ~~vancomycin~~/~~teicoplanin family of antibiotic natural products~~. ~~The X-ray structure of DpgC [Widboom, P~~. ~~W., Fielding, E. N., Liu, Y., and Bruner, S. D. (2007~~) ~~Nature 447~~, 342-345] confirmed the absence of cofactors and defined a novel hydrophobic dioxygen binding pocket adjacent to a bound substrate analogue. In this paper, the role specific amino acids play in substrate recognition and catalysis is ~~examined through biochemical and structural characterization of site-specific enzyme mutations and alternate substrates. The results establish~~ the ~~importance of three amino acids, Arg254, Glu299, and Glu189, in the chemistry of DpgC~~. ~~Arg254 and Glu189 join to form a specific contact with one of the phenolic hydroxyls of the substrate, and this interaction plays a key role in both substrate recognition and catalysis. The X~~-ray crystal structure of Arg254Lys was determined to address the role this residue plays in the chemistry. In addition, characterization of alternate substrate analogues demonstrates the presence and position of phenol groups are necessary for both enzyme recognition and downstream oxidation chemistry. Overall, this work defines the mechanism of substrate recognition and specificity by the cofactor-~~independent dioxygenase DpgC.~~		The line below this paragraph, {{ABSTRACT_PUBMED_18004875}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 18004875 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_18004875}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Ligand binding protein]]		[[Category: Ligand binding protein]]
	[[Category: Protein-ligand complex]]		[[Category: Protein-ligand complex]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13~~:03:09 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 05:11:31 2008''