5xkv - Revision history

OCA at 08:05, 22 November 2023

OCA — Wed, 22 Nov 2023 08:05:32 GMT

←Older revision		Revision as of 08:05, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='5xkv' size='340' side='right'caption='[[5xkv]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='5xkv' size='340' side='right'caption='[[5xkv]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xkv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XKV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.4Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkv OCA], [~~http~~://pdbe.org/5xkv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xkv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xkv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkv ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=5xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkv OCA], [https://pdbe.org/5xkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xkv RCSB], [https://www.ebi.ac.uk/pdbsum/5xkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~MYG_PHYCD MYG_PHYCD]~~] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.	+	[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Yuan, H~~]]	+	[[Category: Physeter catodon]]
-	[[Category: ~~Myoglobin]]~~	+	[[Category: Yuan H]]
-	~~[[Category: Oxygen storage~~]]	+

OCA at 06:53, 14 October 2020

OCA — Wed, 14 Oct 2020 06:53:29 GMT

←Older revision		Revision as of 06:53, 14 October 2020
Line 1:		Line 1:

	==structure of sperm whale myoglobin F138W==		==structure of sperm whale myoglobin F138W==
-	<StructureSection load='5xkv' size='340' side='right' caption='[[5xkv]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='5xkv' size='340' side='right'caption='[[5xkv]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKV OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XKV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XKV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=5xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkv OCA], [http://pdbe.org/5xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkv RCSB], [http://www.ebi.ac.uk/pdbsum/5xkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkv ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkv OCA], [http://pdbe.org/5xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkv RCSB], [http://www.ebi.ac.uk/pdbsum/5xkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Myoglobin\|Myoglobin]]	+	*[[Myoglobin 3D structures\|Myoglobin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Yuan, H]]		[[Category: Yuan, H]]
	[[Category: Myoglobin]]		[[Category: Myoglobin]]
	[[Category: Oxygen storage]]		[[Category: Oxygen storage]]

OCA at 06:39, 18 October 2018

OCA — Thu, 18 Oct 2018 06:39:25 GMT

←Older revision		Revision as of 06:39, 18 October 2018
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5xkv" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xkv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Myoglobin\|Myoglobin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:50, 30 May 2018

OCA — Wed, 30 May 2018 05:50:30 GMT

←Older revision		Revision as of 05:50, 30 May 2018
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.		[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rational design of metalloenzymes provides advantages not only for illustrating the structure and function relationship of native enzymes, but also for creating functional artificial enzymes comparable to native enzymes. Dye-decolorizing peroxidases (DyPs) are a new family of heme peroxidases and have received much attention recently. Inspired by the structural features of native DyPs with multiple Tyr and Trp residues, we herein aimed to design functional artificial DyPs using myoglobin (Mb), an O2 carrier as a protein scaffold, by further introduction of Tyr/Trp into the secondary sphere of the heme center in the F43Y Mb mutant. The latter has been shown to possess a novel Tyr-heme cross-link and exhibit enhanced peroxidase activity, which provides an ideal platform to design a series of derivatives, including F43Y/F46Y Mb, F43Y/I107Y Mb, F43Y/F138 W Mb and F43Y/I107Y/F138 W Mb. Our design revealed that the Tyr-heme cross-link was well-retained in the mutants except for F43Y/F46Y Mb, as confirmed by X-ray crystal structure analysis. More importantly, stopped-flow kinetic studies showed that these derivatives exhibit enhanced dye-decolorizing peroxidase activities compared to that of wild-type (WT) Mb. This is particularly the case for the double mutant F43Y/F138 W Mb, exhibiting an overall catalytic efficiency (kcat/Km) of 110 670 M(-1) s(-1), which is approximately 144-fold and approximately 20-fold that of WT Mb and F43Y Mb, respectively, and is approximately 4.3-fold that of native DyP from Vibrio cholerae. Stopped-flow, electron paramagnetic resonance (EPR) and isothermal titration calorimetry (ITC) studies further provided insights into the activation of H2O2 and the binding of a substrate, reactive blue 19 (RB19), to the double mutant. This study provides valuable information for elucidating the structure and dye-decolorizing function relationship of peroxidases, and also clues for the design of other functional artificial heme enzymes.
		+
		+	Rational design of artificial dye-decolorizing peroxidases using myoglobin by engineering Tyr/Trp in the heme center.,Li LL, Yuan H, Liao F, He B, Gao SQ, Wen GB, Tan X, Lin YW Dalton Trans. 2017 Aug 29;46(34):11230-11238. doi: 10.1039/c7dt02302b. PMID:28795725<ref>PMID:28795725</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xkv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:25, 16 May 2018

OCA — Wed, 16 May 2018 05:25:15 GMT

←Older revision		Revision as of 05:25, 16 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xkv is ~~ON HOLD until Paper Publication~~	+	==structure of sperm whale myoglobin F138W==
-		+	<StructureSection load='5xkv' size='340' side='right' caption='[[5xkv]], [[Resolution\|resolution]] 1.40Å' scene=''>
-	~~Authors~~: ~~Yuan~~, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xkv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XKV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XKV FirstGlance]. <br>
-	~~Description: structure of sperm whale myoglobin F138W~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5xkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xkv OCA], [http://pdbe.org/5xkv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xkv RCSB], [http://www.ebi.ac.uk/pdbsum/5xkv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xkv ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MYG_PHYCD MYG_PHYCD]] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
		+	__TOC__
		+	</StructureSection>
	[[Category: Yuan, H]]		[[Category: Yuan, H]]
		+	[[Category: Myoglobin]]
		+	[[Category: Oxygen storage]]

OCA at 15:32, 27 September 2017

OCA — Wed, 27 Sep 2017 15:32:44 GMT

←Older revision		Revision as of 15:32, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xkv is ON HOLD	+	The entry 5xkv is ON HOLD until Paper Publication

	Authors: Yuan, H.		Authors: Yuan, H.

OCA at 12:34, 24 May 2017

OCA — Wed, 24 May 2017 12:34:15 GMT

←Older revision		Revision as of 12:34, 24 May 2017
Line 3:		Line 3:
	The entry 5xkv is ON HOLD		The entry 5xkv is ON HOLD

-	Authors: Yuan, H	+	Authors: Yuan, H.

	Description: structure of sperm whale myoglobin F138W		Description: structure of sperm whale myoglobin F138W
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yuan, H]]		[[Category: Yuan, H]]

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

OCA — Wed, 17 May 2017 14:54:36 GMT

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

←Older revision

Revision as of 14:54, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xkv is ON HOLD Authors: Yuan, H Description: structure of sperm whale myoglobin F138W Category: Unreleased Structures Category: Yuan, H

OCA — Wed, 17 May 2017 14:54:35 GMT

New page: '''Unreleased structure''' The entry 5xkv is ON HOLD Authors: Yuan, H Description: structure of sperm whale myoglobin F138W Category: Unreleased Structures Category: Yuan, H

New page

'''Unreleased structure'''

The entry 5xkv is ON HOLD

Authors: Yuan, H

Description: structure of sperm whale myoglobin F138W
[[Category: Unreleased Structures]]
[[Category: Yuan, H]]