5w11 - Revision history

OCA at 14:04, 4 October 2023

OCA — Wed, 04 Oct 2023 14:04:45 GMT

←Older revision		Revision as of 14:04, 4 October 2023
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	<StructureSection load='5w11' size='340' side='right'caption='[[5w11]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='5w11' size='340' side='right'caption='[[5w11]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w11]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myceliophthora_thermophila Myceliophthora thermophila~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W11 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W11 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w11]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermothelomyces_thermophilus Thermothelomyces thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W11 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W11 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=~~CTR~~:~~CELLOTRIOSE~~'>~~CTR~~</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.311Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=PRD_900014:alpha-cellotriose'>PRD_900014</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(reducing_end) Cellulose 1,4-beta-cellobiosidase (reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.176 3.2.1.176] </~~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=5w11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w11 OCA], [https://pdbe.org/5w11 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w11 RCSB], [https://www.ebi.ac.uk/pdbsum/5w11 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w11 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=5w11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w11 OCA], [~~http~~://pdbe.org/5w11 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w11 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w11 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w11 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G2Q665_MYCTT G2Q665_MYCTT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myceliophthora thermophila]]~~	+	[[Category: Thermothelomyces thermophilus]]
-	~~[[Category: Godoy, M O.de~~]]	+	[[Category: Higasi P]]
-	[[Category: Higasi, P]]	+	[[Category: Kadowaki MAS]]
-	[[Category: Kadowaki~~, M A.S~~]]	+	[[Category: Polikarpov I]]
-	[[Category: Polikarpov, I]]	+	[[Category: Prade RA]]
-	[[Category: Prade~~, R A~~]]	+	[[Category: De Godoy MO]]
-	[[Category: ~~Cellobiohydrolase]]~~	+
-	~~[[Category: Cellulase]]~~	+
-	~~[[Category: Extracellular]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:44, 1 January 2020

OCA — Wed, 01 Jan 2020 09:44:10 GMT

←Older revision		Revision as of 09:44, 1 January 2020
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	==See Also==		==See Also==
-	*[[Cellobiohydrolase\|Cellobiohydrolase]]	+	*[[Cellobiohydrolase 3D structures\|Cellobiohydrolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:30, 17 April 2019

OCA — Wed, 17 Apr 2019 06:30:50 GMT

←Older revision		Revision as of 06:30, 17 April 2019
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	==Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus Myceliophthora thermophila==		==Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus Myceliophthora thermophila==
-	<StructureSection load='5w11' size='340' side='right' caption='[[5w11]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='5w11' size='340' side='right'caption='[[5w11]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5w11]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myceliophthora_thermophila Myceliophthora thermophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W11 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5w11]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myceliophthora_thermophila Myceliophthora thermophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W11 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5w11" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w11" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cellobiohydrolase\|Cellobiohydrolase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Myceliophthora thermophila]]		[[Category: Myceliophthora thermophila]]
	[[Category: Godoy, M O.de]]		[[Category: Godoy, M O.de]]

OCA at 06:42, 20 December 2017

OCA — Wed, 20 Dec 2017 06:42:54 GMT

←Older revision		Revision as of 06:42, 20 December 2017
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	<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=5w11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w11 OCA], [http://pdbe.org/5w11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w11 RCSB], [http://www.ebi.ac.uk/pdbsum/5w11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w11 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=5w11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w11 OCA], [http://pdbe.org/5w11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w11 RCSB], [http://www.ebi.ac.uk/pdbsum/5w11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w11 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by beta-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent the access of hydrolytic enzymes and water molecules. The most abundant enzyme secreted by Myceliophthora thermophila M77 in response to the presence of biomass is the cellobiohydrolase MtCel7A, which is composed by a GH7-catalytic domain (CD), a linker and a CBM1-type carbohydrate binding module. GH7 cellobiohydrolases have been studied before and structural models have been proposed. However, current available GH7 crystal structures only define separate catalytic domains and/or cellulose-binding modules and do not include the full length structures that are involved in shaping the catalytic mode of operation. In this study, we determined the 3D-structure of catalytic domain using X-ray crystallography and retrieved the full length enzyme envelope via small-angle X-ray scattering (SAXS) technique. The SAXS data reveal a tadpole-like molecular shape with a rigid linker connecting the CD and CBM. Our biochemical studies show that MtCel7A has higher catalytic efficiency and thermostability as well as lower processivity when compared to the well-studied TrCel7A from Trichoderma reesei. Based on a comparison of the crystallographic structures of CDs and their molecular dynamic simulations, we demonstrate that MtCel7A has considerably higher flexibility than TrCel7A. In particular, loops that cover the active site are more flexible and undergo higher conformational fluctuations, which might account for decreased processivity and enhanced enzymatic efficiency. Our statistical coupling analysis (SCA) suggests co-evolution of amino acid clusters comprising the catalytic site of MtCel7A, which correlate with the steps in the catalytic cycle of the enzyme. This article is protected by copyright. All rights reserved.
		+
		+	Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila.,Kadowaki MAS, Higasi P, de Godoy MO, Prade RA, Polikarpov I FEBS J. 2017 Dec 8. doi: 10.1111/febs.14356. PMID:29222836<ref>PMID:29222836</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5w11" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:58, 13 December 2017

OCA — Wed, 13 Dec 2017 06:58:13 GMT

←Older revision		Revision as of 06:58, 13 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5w11 ~~is ON HOLD until Paper Publication~~	+	==Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus Myceliophthora thermophila==
-		+	<StructureSection load='5w11' size='340' side='right' caption='[[5w11]], [[Resolution\|resolution]] 2.31Å' scene=''>
-	~~Authors~~: ~~Kadowaki, M~~.A.S., ~~Higasi~~, P., ~~de Godoy~~, M.O., ~~Prade~~, R.A., ~~Polikarpov~~, I.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5w11]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myceliophthora_thermophila Myceliophthora thermophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W11 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W11 FirstGlance]. <br>
-	~~Description~~: ~~Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus~~ Myceliophthora thermophila	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=144:TRIS-HYDROXYMETHYL-METHYL-AMMONIUM'>144</scene>, <scene name='pdbligand=CTR:CELLOTRIOSE'>CTR</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulose_1,4-beta-cellobiosidase_(reducing_end) Cellulose 1,4-beta-cellobiosidase (reducing end)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.176 3.2.1.176] </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=5w11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w11 OCA], [http://pdbe.org/5w11 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w11 RCSB], [http://www.ebi.ac.uk/pdbsum/5w11 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w11 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Myceliophthora thermophila]]
		+	[[Category: Godoy, M O.de]]
		+	[[Category: Higasi, P]]
		+	[[Category: Kadowaki, M A.S]]
	[[Category: Polikarpov, I]]		[[Category: Polikarpov, I]]
-	[[Category: ~~De Godoy~~, ~~M.O~~]]	+	[[Category: Prade, R A]]
-	[[Category: ~~Higasi, P~~]]	+	[[Category: Cellobiohydrolase]]
-	[[Category: ~~Prade, R.A~~]]	+	[[Category: Cellulase]]
-	[[Category: ~~Kadowaki, M.A.S~~]]	+	[[Category: Extracellular]]
		+	[[Category: Hydrolase]]

OCA: Protected "5w11" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:19:08 GMT

Protected "5w11" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:19, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5w11 is ON HOLD until Paper Publication Authors: Kadowaki, M.A.S., Higasi, P., de Godoy, M.O., Prade, R.A., Polikarpov, I. Description: Biochemical...

OCA — Wed, 27 Sep 2017 14:19:07 GMT

New page: '''Unreleased structure''' The entry 5w11 is ON HOLD until Paper Publication Authors: Kadowaki, M.A.S., Higasi, P., de Godoy, M.O., Prade, R.A., Polikarpov, I. Description: Biochemical...

New page

'''Unreleased structure'''

The entry 5w11 is ON HOLD until Paper Publication

Authors: Kadowaki, M.A.S., Higasi, P., de Godoy, M.O., Prade, R.A., Polikarpov, I.

Description: Biochemical and structural insights into the catalytic mechanism of thermostable cellobiohydrolase Cel7A from industrially relevant fungus Myceliophthora thermophila
[[Category: Unreleased Structures]]
[[Category: Polikarpov, I]]
[[Category: De Godoy, M.O]]
[[Category: Higasi, P]]
[[Category: Prade, R.A]]
[[Category: Kadowaki, M.A.S]]