6i3l - Revision history

OCA at 07:35, 1 May 2024

2024-05-01T07:35:23Z

←Older revision		Revision as of 07:35, 1 May 2024
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	<StructureSection load='6i3l' size='340' side='right'caption='[[6i3l]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6i3l' size='340' side='right'caption='[[6i3l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i3l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I3L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i3l]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Albifimbria_verrucaria Albifimbria verrucaria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I3L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6i3j\|6i3j]], [[6i3k\|6i3k]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bilirubin_oxidase Bilirubin oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.5 1.3.3.5] </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=6i3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3l OCA], [https://pdbe.org/6i3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i3l RCSB], [https://www.ebi.ac.uk/pdbsum/6i3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3l ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6i3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3l OCA], [~~http~~://pdbe.org/6i3l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i3l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i3l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3l ProSAT]</span></td></tr>	+
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/BLRO_ALBVE BLRO_ALBVE]
-	Unlike any protein studied so far, the active site of bilirubin oxidase from Myrothecium verrucaria contains a unique type of covalent link between tryptophan and histidine side chains. The role of this post-translational modification in substrate binding and oxidation is not sufficiently understood. Our structural and mutational studies provide evidence that this Trp396-His398 adduct modifies T1 copper coordination and is an important part of the substrate binding and oxidation site. The presence of the adduct is crucial for oxidation of substituted phenols and it substantially influences the rate of oxidation of bilirubin. Additionally, we bring the first structure of bilirubin oxidase in complex with one of its products, ferricyanide ion, interacting with the modified tryptophan side chain, Arg356 and the active site-forming loop 393-398. The results imply that structurally and chemically distinct types of substrates, including bilirubin, utilize the Trp-His adduct mainly for binding and to a smaller extent for electron transfer.	+
-		+
-	Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.,Koval T, Svecova L, Ostergaard LH, Skalova T, Duskova J, Hasek J, Kolenko P, Fejfarova K, Stransky J, Trundova M, Dohnalek J Sci Rep. 2019 Sep 23;9(1):~~13700. doi: 10.1038~~/~~s41598-019-50105-3. PMID:31548583<ref>PMID:31548583<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6i3l" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bilirubin oxidase~~]]	+	[[Category: Albifimbria verrucaria]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dohnalek, J]]	+	[[Category: Dohnalek J]]
-	[[Category: Duskova, J]]	+	[[Category: Duskova J]]
-	[[Category: Kolenko, P]]	+	[[Category: Kolenko P]]
-	[[Category: Koval, T]]	+	[[Category: Koval T]]
-	[[Category: Ostergaard~~, L H~~]]	+	[[Category: Ostergaard LH]]
-	[[Category: Skalova, T]]	+	[[Category: Skalova T]]
-	[[Category: Svecova, L]]	+	[[Category: Svecova L]]
-	~~[[Category: Enzymatic activity]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:19, 2 October 2019

2019-10-02T10:19:31Z

←Older revision		Revision as of 10:19, 2 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6i3l is ~~ON HOLD until Paper~~ Publication	+	==Bilirubin oxidase from Myrothecium verrucaria, mutant W396F==
		+	<StructureSection load='6i3l' size='340' side='right'caption='[[6i3l]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i3l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I3L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6i3j\|6i3j]], [[6i3k\|6i3k]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Bilirubin_oxidase Bilirubin oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.5 1.3.3.5] </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=6i3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3l OCA], [http://pdbe.org/6i3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i3l RCSB], [http://www.ebi.ac.uk/pdbsum/6i3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3l ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Unlike any protein studied so far, the active site of bilirubin oxidase from Myrothecium verrucaria contains a unique type of covalent link between tryptophan and histidine side chains. The role of this post-translational modification in substrate binding and oxidation is not sufficiently understood. Our structural and mutational studies provide evidence that this Trp396-His398 adduct modifies T1 copper coordination and is an important part of the substrate binding and oxidation site. The presence of the adduct is crucial for oxidation of substituted phenols and it substantially influences the rate of oxidation of bilirubin. Additionally, we bring the first structure of bilirubin oxidase in complex with one of its products, ferricyanide ion, interacting with the modified tryptophan side chain, Arg356 and the active site-forming loop 393-398. The results imply that structurally and chemically distinct types of substrates, including bilirubin, utilize the Trp-His adduct mainly for binding and to a smaller extent for electron transfer.

-	~~Authors~~:	+	Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.,Koval T, Svecova L, Ostergaard LH, Skalova T, Duskova J, Hasek J, Kolenko P, Fejfarova K, Stransky J, Trundova M, Dohnalek J Sci Rep. 2019 Sep 23;9(1):13700. doi: 10.1038/s41598-019-50105-3. PMID:31548583<ref>PMID:31548583</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6i3l" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bilirubin oxidase]]
		+	[[Category: Large Structures]]
		+	[[Category: Dohnalek, J]]
		+	[[Category: Duskova, J]]
		+	[[Category: Kolenko, P]]
		+	[[Category: Koval, T]]
		+	[[Category: Ostergaard, L H]]
		+	[[Category: Skalova, T]]
		+	[[Category: Svecova, L]]
		+	[[Category: Enzymatic activity]]
		+	[[Category: Mutant]]
		+	[[Category: Oxidoreductase]]

OCA at 18:31, 2 December 2018

2018-12-02T18:31:18Z

←Older revision		Revision as of 18:31, 2 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6i3l is ON HOLD	+	The entry 6i3l is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6i3l" [edit=sysop:move=sysop]

2018-11-14T06:21:13Z

Protected "6i3l" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:21, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6i3l is ON HOLD Authors: Description: Category: Unreleased Structures

2018-11-14T06:21:12Z

New page: '''Unreleased structure''' The entry 6i3l is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6i3l is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]