2rts - Revision history

OCA at 07:06, 1 May 2024

2024-05-01T07:06:29Z

←Older revision		Revision as of 07:06, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTS FirstGlance]. <br>
-	</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [https://pdbe.org/2rts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [https://www.ebi.ac.uk/pdbsum/2rts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [https://pdbe.org/2rts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [https://www.ebi.ac.uk/pdbsum/2rts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q8U1H4_PYRFU Q8U1H4_PYRFU]		[https://www.uniprot.org/uniprot/Q8U1H4_PYRFU Q8U1H4_PYRFU]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A chitinase, from Pyrococcus furiosus, is a hyperthermophilic glycosidase that effectively hydrolyses both alpha and beta crystalline chitin. This chitinase has unique structural features; it contains two catalytic domains (AD1 and AD2) and two chitin-binding domains (ChBD1 and ChBD2). We have determined the structure of ChBD1, which significantly enhances the activity of the catalytic domains, by nuclear magnetic resonance spectroscopy. The overall structure of ChBD1 had a compact and globular architecture consisting of three anti-parallel beta-strands, similar to those of other proteins classified into carbohydrate-binding module (CBM) family 5. A mutagenesis experiment suggested three solvent-exposed aromatic residues (Tyr112, Trp113 and Tyr123) as the chitin-binding sites. The involvement of Tyr123 or the corresponding aromatic residues in other CBMs, has been demonstrated for the first time. This result indicates that the binding mode may be different from those of other chitin-binding domains in CBM family 5. In addition, the binding affinities of ChBD1 and ChBD2 were quite different, suggesting that the two ChBDs each play a different role in efficiently increasing the activities of AD1 and AD2.
-
-	Solution structure of the chitin-binding domain 1 (ChBD1) of a hyperthermophilic chitinase from Pyrococcus furiosus.,Mine S, Nakamura T, Sato T, Ikegami T, Uegaki K J Biochem. 2014 Feb;155(2):115-22. doi: 10.1093/jb/mvt104. Epub 2013 Nov 21. PMID:24272751<ref>PMID:24272751</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2rts" style="background-color:#fffaf0;"></div>

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

OCA at 20:52, 12 April 2023

2023-04-12T20:52:36Z

←Older revision		Revision as of 20:52, 12 April 2023
Line 1:		Line 1:

	==Chitin binding domain1==		==Chitin binding domain1==
-	<StructureSection load='2rts' size='340' side='right'caption='[[2rts~~]], [[NMR_Ensembles_of_Models \| 30 NMR models~~]]' scene=''>	+	<StructureSection load='2rts' size='340' side='right'caption='[[2rts]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTS FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>~~	+	</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [https://pdbe.org/2rts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [https://www.ebi.ac.uk/pdbsum/2rts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts 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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [https://pdbe.org/2rts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [https://www.ebi.ac.uk/pdbsum/2rts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8U1H4_PYRFU Q8U1H4_PYRFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Uegaki, K]]	+	[[Category: Uegaki K]]
-	~~[[Category: Chitin binding domain]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 10:36, 7 July 2021

2021-07-07T10:36:38Z

←Older revision		Revision as of 10:36, 7 July 2021
Line 1:		Line 1:

	==Chitin binding domain1==		==Chitin binding domain1==
-	<StructureSection load='2rts' size='340' side='right' caption='[[2rts]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>	+	<StructureSection load='2rts' size='340' side='right'caption='[[2rts]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RTS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RTS FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [~~http~~://pdbe.org/2rts PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rts PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts 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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [https://pdbe.org/2rts PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [https://www.ebi.ac.uk/pdbsum/2rts PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:

	==See Also==		==See Also==
-	*[[Chitinase\|Chitinase]]	+	*[[Chitinase 3D structures\|Chitinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
	[[Category: Uegaki, K]]		[[Category: Uegaki, K]]
	[[Category: Chitin binding domain]]		[[Category: Chitin binding domain]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 17:43, 5 August 2016

2016-08-05T17:43:22Z

←Older revision		Revision as of 17:43, 5 August 2016
Line 1:		Line 1:
		+
	==Chitin binding domain1==		==Chitin binding domain1==
	<StructureSection load='2rts' size='340' side='right' caption='[[2rts]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>		<StructureSection load='2rts' size='340' side='right' caption='[[2rts]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RTS FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RTS FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [http://www.ebi.ac.uk/pdbsum/2rts 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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [http://pdbe.org/2rts PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [http://www.ebi.ac.uk/pdbsum/2rts PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rts ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 2rts" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Chitinase\|Chitinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:09, 3 January 2015

2015-01-03T23:09:35Z

←Older revision		Revision as of 23:09, 3 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_2rts~~\| ~~PDB~~=2rts \| ~~SCENE~~= }}	+	==Chitin binding domain1==
-	===~~Chitin binding domain1~~===	+	<StructureSection load='2rts' size='340' side='right' caption='[[2rts]], [[NMR_Ensembles_of_Models \| 30 NMR models]]' scene=''>
-	~~{{ABSTRACT_PUBMED_24272751}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rts]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RTS FirstGlance]. <br>
		+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1234 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=2rts FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rts OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rts RCSB], [http://www.ebi.ac.uk/pdbsum/2rts PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A chitinase, from Pyrococcus furiosus, is a hyperthermophilic glycosidase that effectively hydrolyses both alpha and beta crystalline chitin. This chitinase has unique structural features; it contains two catalytic domains (AD1 and AD2) and two chitin-binding domains (ChBD1 and ChBD2). We have determined the structure of ChBD1, which significantly enhances the activity of the catalytic domains, by nuclear magnetic resonance spectroscopy. The overall structure of ChBD1 had a compact and globular architecture consisting of three anti-parallel beta-strands, similar to those of other proteins classified into carbohydrate-binding module (CBM) family 5. A mutagenesis experiment suggested three solvent-exposed aromatic residues (Tyr112, Trp113 and Tyr123) as the chitin-binding sites. The involvement of Tyr123 or the corresponding aromatic residues in other CBMs, has been demonstrated for the first time. This result indicates that the binding mode may be different from those of other chitin-binding domains in CBM family 5. In addition, the binding affinities of ChBD1 and ChBD2 were quite different, suggesting that the two ChBDs each play a different role in efficiently increasing the activities of AD1 and AD2.

-	~~==About this Structure==~~	+	Solution structure of the chitin-binding domain 1 (ChBD1) of a hyperthermophilic chitinase from Pyrococcus furiosus.,Mine S, Nakamura T, Sato T, Ikegami T, Uegaki K J Biochem. 2014 Feb;155(2):115-22. doi: 10.1093/jb/mvt104. Epub 2013 Nov 21. PMID:24272751<ref>PMID:24272751</ref>
-	~~[[2rts]] is a 1 chain~~ structure~~. Full experimental information is available~~ from ~~[http://oca~~.~~weizmann~~.ac.il/~~oca-bin~~/~~ocashort?id=2RTS OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024272751</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Uegaki, K.]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Pyrfu]]
		+	[[Category: Uegaki, K]]
	[[Category: Chitin binding domain]]		[[Category: Chitin binding domain]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 07:38, 23 April 2014

2014-04-23T07:38:48Z

←Older revision		Revision as of 07:38, 23 April 2014
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_2rts\| PDB=2rts \| SCENE= }}
		+	===Chitin binding domain1===
		+	{{ABSTRACT_PUBMED_24272751}}

-	~~The entry~~ 2rts is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[2rts]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RTS OCA].

-	~~Authors~~: Uegaki, K.	+	==Reference==
-		+	<ref group="xtra">PMID:024272751</ref><references group="xtra"/><references/>
-	~~Description~~: Chitin binding ~~domain1~~	+	[[Category: Uegaki, K.]]
		+	[[Category: Chitin binding domain]]
		+	[[Category: Hydrolase]]

OCA at 05:21, 10 October 2013

2013-10-10T05:21:14Z

←Older revision		Revision as of 05:21, 10 October 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 2rts is ON HOLD	+	The entry 2rts is ON HOLD until Paper Publication

	Authors: Uegaki, K.		Authors: Uegaki, K.

	Description: Chitin binding domain1		Description: Chitin binding domain1

OCA at 03:11, 20 September 2013

2013-09-20T03:11:18Z

←Older revision		Revision as of 03:11, 20 September 2013
Line 5:		Line 5:
	Authors: Uegaki, K.		Authors: Uegaki, K.

-	Description: ~~chitin~~ binding domain1	+	Description: Chitin binding domain1

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

2013-09-04T09:20:49Z

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

←Older revision

Revision as of 09:20, 4 September 2013

OCA: New page: '''Unreleased structure''' The entry 2rts is ON HOLD Authors: Uegaki, K. Description: chitin binding domain1

2013-09-04T09:20:48Z

New page: '''Unreleased structure''' The entry 2rts is ON HOLD Authors: Uegaki, K. Description: chitin binding domain1

New page

'''Unreleased structure'''

The entry 2rts is ON HOLD

Authors: Uegaki, K.

Description: chitin binding domain1