4ghf - Revision history

OCA at 15:46, 14 March 2024

OCA — Thu, 14 Mar 2024 15:46:59 GMT

←Older revision		Revision as of 15:46, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GHF FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GHF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</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]] 1.67Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [https://pdbe.org/4ghf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [https://www.ebi.ac.uk/pdbsum/4ghf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ghf 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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [https://pdbe.org/4ghf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [https://www.ebi.ac.uk/pdbsum/4ghf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ghf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q45135_9MICO Q45135_9MICO]		[https://www.uniprot.org/uniprot/Q45135_9MICO Q45135_9MICO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Homoprotocatechuate 2,3-dioxygenase (FeHPCD) utilizes an active site Fe(II) to activate O(2) in a reaction cycle that ultimately results in aromatic ring cleavage. Here, the roles of the conserved active site residue Tyr257 are investigated by solving the X-ray crystal structures of the Tyr257-to-Phe variant (Y257F) in complex with the substrate homoprotocatechuate (HPCA) and the alternative substrate 4-nitrocatechol (4NC). These are compared with structures of the analogous wild type enzyme complexes. In addition, the oxy intermediate of the reaction cycle of Y257F-4NC + O(2) is formed in crystallo and structurally characterized. It is shown that both substrates adopt a previously unrecognized, slightly nonplanar, strained conformation affecting the geometries of all aromatic ring carbons when bound in the FeHPCD active site. This global deviation from planarity is not observed for the Y257F variant. In the Y257F-4NC-oxy complex, the O(2) is bound side-on to the Fe(II), while the 4NC is chelated in two adjacent sites. The ring of the 4NC in this complex is planar, in contrast to the equivalent FeHPCD intermediate, which exhibits substantial local distortion of the substrate hydroxyl moiety (C2-O(-)) that is hydrogen bonded to Tyr257. We propose that Tyr257 induces the global and local distortions of the substrate ring in two different ways. First, van der Waals conflict between the Tyr257-OH substituent and the substrate C2 carbon is relieved by adopting the globally strained structure. Second, Tyr257 stabilizes the localized out-of-plane position of the C2-O(-) by forming a stronger hydrogen bond as the distortion increases. Both types of distortions favor transfer of one electron out of the substrate to form a reactive semiquinone radical. Then, the localized distortion at substrate C2 promotes formation of the key alkylperoxo intermediate of the cycle resulting from oxygen attack on the activated substrate at C2, which becomes sp(3) hybridized. The inability of Y257F to promote the distorted substrate structure may explain the observed 100-fold decrease in the rates of the O(2) activation and insertion steps of the reaction.
-
-	Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation.,Kovaleva EG, Lipscomb JD Biochemistry. 2012 Nov 6;51(44):8755-63. doi: 10.1021/bi301115c. Epub 2012 Oct, 29. PMID:23066739<ref>PMID:23066739</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ghf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]		*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:56, 26 October 2022

OCA — Wed, 26 Oct 2022 06:56:53 GMT

←Older revision		Revision as of 06:56, 26 October 2022
Line 1:		Line 1:

	==Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution==		==Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution==
-	<StructureSection load='4ghf' size='340' side='right' caption='[[4ghf]], [[Resolution\|resolution]] 1.67Å' scene=''>	+	<StructureSection load='4ghf' size='340' side='right'caption='[[4ghf]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~'brevibacterium_fuscum' 'brevibacterium~~ fuscum']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GHF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GHF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ghc\|4ghc]], [[4ghd\|4ghd]], [[4ghe\|4ghe]], [[4ghg\|4ghg]], [[4ghh\|4ghh]]</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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [https://pdbe.org/4ghf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [https://www.ebi.ac.uk/pdbsum/4ghf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ghf ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 'Brevibacterium fuscum'])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [~~http~~://pdbe.org/4ghf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ghf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ghf ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q45135_9MICO Q45135_9MICO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Dioxygenase\|Dioxygenase]]	+	*[[Dioxygenase 3D structures\|Dioxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Brevibacterium fuscum]]		[[Category: Brevibacterium fuscum]]
-	[[Category: ~~3,4-dihydroxyphenylacetate 2,3-dioxygenase~~]]	+	[[Category: Large Structures]]
-	[[Category: Kovaleva~~, E G~~]]	+	[[Category: Kovaleva EG]]
-	[[Category: Lipscomb~~, J D]]~~	+	[[Category: Lipscomb JD]]
-	~~[[Category: 2-his-1-carboxylate facial triad]]~~	+
-	~~[[Category: 4-nitrocatechol]]~~	+
-	~~[[Category: Dioxygenase]]~~	+
-	~~[[Category: Homoprotocatechuate]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxy complex]]~~	+
-	~~[[Category: Oxygen activation~~]]	+

OCA at 20:03, 15 December 2016

OCA — Thu, 15 Dec 2016 20:03:42 GMT

←Older revision		Revision as of 20:03, 15 December 2016
Line 1:		Line 1:
		+
	==Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution==		==Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution==
	<StructureSection load='4ghf' size='340' side='right' caption='[[4ghf]], [[Resolution\|resolution]] 1.67Å' scene=''>		<StructureSection load='4ghf' size='340' side='right' caption='[[4ghf]], [[Resolution\|resolution]] 1.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Brevibacterium_fuscum Brevibacterium~~ fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GHF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/'brevibacterium_fuscum' 'brevibacterium fuscum']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GHF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ghc\|4ghc]], [[4ghd\|4ghd]], [[4ghe\|4ghe]], [[4ghg\|4ghg]], [[4ghh\|4ghh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ghc\|4ghc]], [[4ghd\|4ghd]], [[4ghe\|4ghe]], [[4ghg\|4ghg]], [[4ghh\|4ghh]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 Brevibacterium fuscum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 'Brevibacterium fuscum'])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [http://www.ebi.ac.uk/pdbsum/4ghf 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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [http://pdbe.org/4ghf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [http://www.ebi.ac.uk/pdbsum/4ghf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ghf ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4ghf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 24:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
	[[Category: Brevibacterium fuscum]]		[[Category: Brevibacterium fuscum]]
		+	[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
	[[Category: Kovaleva, E G]]		[[Category: Kovaleva, E G]]
	[[Category: Lipscomb, J D]]		[[Category: Lipscomb, J D]]

OCA at 09:43, 10 December 2014

OCA — Wed, 10 Dec 2014 09:43:30 GMT

←Older revision		Revision as of 09:43, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4ghf.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution==
		+	<StructureSection load='4ghf' size='340' side='right' caption='[[4ghf]], [[Resolution\|resolution]] 1.67Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ghf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GHF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4NC:4-NITROCATECHOL'>4NC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ghc\|4ghc]], [[4ghd\|4ghd]], [[4ghe\|4ghe]], [[4ghg\|4ghg]], [[4ghh\|4ghh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hpcd ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=47914 Brevibacterium fuscum])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3,4-dihydroxyphenylacetate_2,3-dioxygenase 3,4-dihydroxyphenylacetate 2,3-dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.15 1.13.11.15] </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=4ghf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ghf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ghf RCSB], [http://www.ebi.ac.uk/pdbsum/4ghf PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Homoprotocatechuate 2,3-dioxygenase (FeHPCD) utilizes an active site Fe(II) to activate O(2) in a reaction cycle that ultimately results in aromatic ring cleavage. Here, the roles of the conserved active site residue Tyr257 are investigated by solving the X-ray crystal structures of the Tyr257-to-Phe variant (Y257F) in complex with the substrate homoprotocatechuate (HPCA) and the alternative substrate 4-nitrocatechol (4NC). These are compared with structures of the analogous wild type enzyme complexes. In addition, the oxy intermediate of the reaction cycle of Y257F-4NC + O(2) is formed in crystallo and structurally characterized. It is shown that both substrates adopt a previously unrecognized, slightly nonplanar, strained conformation affecting the geometries of all aromatic ring carbons when bound in the FeHPCD active site. This global deviation from planarity is not observed for the Y257F variant. In the Y257F-4NC-oxy complex, the O(2) is bound side-on to the Fe(II), while the 4NC is chelated in two adjacent sites. The ring of the 4NC in this complex is planar, in contrast to the equivalent FeHPCD intermediate, which exhibits substantial local distortion of the substrate hydroxyl moiety (C2-O(-)) that is hydrogen bonded to Tyr257. We propose that Tyr257 induces the global and local distortions of the substrate ring in two different ways. First, van der Waals conflict between the Tyr257-OH substituent and the substrate C2 carbon is relieved by adopting the globally strained structure. Second, Tyr257 stabilizes the localized out-of-plane position of the C2-O(-) by forming a stronger hydrogen bond as the distortion increases. Both types of distortions favor transfer of one electron out of the substrate to form a reactive semiquinone radical. Then, the localized distortion at substrate C2 promotes formation of the key alkylperoxo intermediate of the cycle resulting from oxygen attack on the activated substrate at C2, which becomes sp(3) hybridized. The inability of Y257F to promote the distorted substrate structure may explain the observed 100-fold decrease in the rates of the O(2) activation and insertion steps of the reaction.

-	~~{{STRUCTURE_4ghf\| PDB=4ghf \| SCENE= }}~~	+	Structural basis for the role of tyrosine 257 of homoprotocatechuate 2,3-dioxygenase in substrate and oxygen activation.,Kovaleva EG, Lipscomb JD Biochemistry. 2012 Nov 6;51(44):8755-63. doi: 10.1021/bi301115c. Epub 2012 Oct, 29. PMID:23066739<ref>PMID:23066739</ref>

-	~~===Structure of Y257F variant of Homoprotocatechuate 2~~,~~3-Dioxygenase from B~~.~~fuscum in complex with 4-Nitrocatechol and dioxygen at 1~~.~~67 Ang resolution===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_23066739}}~~	+	==See Also==
-		+	*[[Dioxygenase\|Dioxygenase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4ghf~~]] ~~is a 4 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA].~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]		[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
	[[Category: Brevibacterium fuscum]]		[[Category: Brevibacterium fuscum]]
-	[[Category: Kovaleva, E G.]]	+	[[Category: Kovaleva, E G]]
-	[[Category: Lipscomb, J D.]]	+	[[Category: Lipscomb, J D]]
	[[Category: 2-his-1-carboxylate facial triad]]		[[Category: 2-his-1-carboxylate facial triad]]
	[[Category: 4-nitrocatechol]]		[[Category: 4-nitrocatechol]]

OCA at 21:34, 12 December 2012

OCA — Wed, 12 Dec 2012 21:34:05 GMT

←Older revision		Revision as of 21:34, 12 December 2012
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-	[[Image:4ghf.~~jpg~~\|left\|200px]]	+	[[Image:4ghf.png\|left\|200px]]

	{{STRUCTURE_4ghf\| PDB=4ghf \| SCENE= }}		{{STRUCTURE_4ghf\| PDB=4ghf \| SCENE= }}

OCA at 09:03, 31 October 2012

OCA — Wed, 31 Oct 2012 09:03:19 GMT

←Older revision		Revision as of 09:03, 31 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4ghf.jpg\|left\|200px]]

-	~~The entry~~ 4ghf ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4ghf\| PDB=4ghf \| SCENE= }}

-	~~Authors: Kovaleva~~, E.~~G., Lipscomb, J.D~~.	+	===Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution===

-	~~Description:~~ Structure ~~of Y257F variant of Homoprotocatechuate~~ 2,3-~~Dioxygenase from B.~~fuscum ~~in complex with 4~~-~~Nitrocatechol and dioxygen at~~ 1~~.67 Ang resolution~~	+	{{ABSTRACT_PUBMED_23066739}}
		+
		+	==About this Structure==
		+	[[4ghf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Brevibacterium_fuscum Brevibacterium fuscum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GHF OCA].
		+	[[Category: 3,4-dihydroxyphenylacetate 2,3-dioxygenase]]
		+	[[Category: Brevibacterium fuscum]]
		+	[[Category: Kovaleva, E G.]]
		+	[[Category: Lipscomb, J D.]]
		+	[[Category: 2-his-1-carboxylate facial triad]]
		+	[[Category: 4-nitrocatechol]]
		+	[[Category: Dioxygenase]]
		+	[[Category: Homoprotocatechuate]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxy complex]]
		+	[[Category: Oxygen activation]]

OCA at 06:52, 19 September 2012

OCA — Wed, 19 Sep 2012 06:52:08 GMT

←Older revision		Revision as of 06:52, 19 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ghf is ON HOLD	+	The entry 4ghf is ON HOLD until Paper Publication

	Authors: Kovaleva, E.G., Lipscomb, J.D.		Authors: Kovaleva, E.G., Lipscomb, J.D.

	Description: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution		Description: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution

OCA: Protected "4ghf" [edit=sysop:move=sysop]

OCA — Wed, 15 Aug 2012 05:26:37 GMT

Protected "4ghf" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:26, 15 August 2012

OCA: New page: '''Unreleased structure''' The entry 4ghf is ON HOLD Authors: Kovaleva, E.G., Lipscomb, J.D. Description: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscu...

OCA — Wed, 15 Aug 2012 05:26:36 GMT

New page: '''Unreleased structure''' The entry 4ghf is ON HOLD Authors: Kovaleva, E.G., Lipscomb, J.D. Description: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscu...

New page

'''Unreleased structure'''

The entry 4ghf is ON HOLD

Authors: Kovaleva, E.G., Lipscomb, J.D.

Description: Structure of Y257F variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-Nitrocatechol and dioxygen at 1.67 Ang resolution