6n2b - Revision history

OCA at 06:43, 11 October 2023

2023-10-11T06:43:43Z

←Older revision		Revision as of 06:43, 11 October 2023
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	<StructureSection load='6n2b' size='340' side='right'caption='[[6n2b]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6n2b' size='340' side='right'caption='[[6n2b]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2b]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Calki Calki~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2b]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldicellulosiruptor_kristjanssonii_I77R1B Caldicellulosiruptor kristjanssonii I77R1B]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N2B FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.65Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Calkr_0826 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=632335 CALKI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6n2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2b OCA], [~~http~~://pdbe.org/6n2b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n2b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n2b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2b 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=6n2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2b OCA], [https://pdbe.org/6n2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n2b RCSB], [https://www.ebi.ac.uk/pdbsum/6n2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2b ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E4S4B2_CALKI E4S4B2_CALKI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Calki~~]]	+	[[Category: Caldicellulosiruptor kristjanssonii I77R1B]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Alahuhta~~, P M~~]]	+	[[Category: Alahuhta PM]]
-	[[Category: Lunin~~, V V]]~~	+	[[Category: Lunin VV]]
-	~~[[Category: Beta-helix]]~~	+
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Cellulose binding~~]]	+

OCA at 10:28, 4 December 2019

2019-12-04T10:28:41Z

←Older revision		Revision as of 10:28, 4 December 2019
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	==The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain==		==The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain==
-	<StructureSection load='6n2b' size='340' side='right' caption='[[6n2b]], [[Resolution\|resolution]] 2.65Å' scene=''>	+	<StructureSection load='6n2b' size='340' side='right'caption='[[6n2b]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n2b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n2b]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Calki Calki]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2B FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Calkr_0826 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=632335 CALKI])</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=6n2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2b OCA], [http://pdbe.org/6n2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2b RCSB], [http://www.ebi.ac.uk/pdbsum/6n2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2b 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=6n2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2b OCA], [http://pdbe.org/6n2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2b RCSB], [http://www.ebi.ac.uk/pdbsum/6n2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2b ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Calki]]
		+	[[Category: Large Structures]]
	[[Category: Alahuhta, P M]]		[[Category: Alahuhta, P M]]
	[[Category: Lunin, V V]]		[[Category: Lunin, V V]]

OCA at 08:35, 19 December 2018

2018-12-19T08:35:59Z

←Older revision		Revision as of 08:35, 19 December 2018
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-	'''Unreleased structure'''

-	The ~~entry~~ 6n2b is ~~ON HOLD until Paper~~ Publication	+	==The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain==
		+	<StructureSection load='6n2b' size='340' side='right' caption='[[6n2b]], [[Resolution\|resolution]] 2.65Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n2b]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N2B FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6n2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n2b OCA], [http://pdbe.org/6n2b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n2b RCSB], [http://www.ebi.ac.uk/pdbsum/6n2b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n2b ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genomes of extremely thermophilic Caldicellulosiruptor species encode novel cellulose binding proteins, tapirins, located proximate to the type IV pilus locus. The C-terminal domain of a tapirin (Calkro_0844) from Caldicellulosiruptor kronotskyensis is structurally unique and has a cellulose binding affinity akin to family 3 carbohydrate binding modules (CBM3). Here, full-length and C-terminal versions of tapirins from Caldicellulosiruptor bescii (Athe_1870), Caldicellulosiruptor hydrothermalis (Calhy_0908), Caldicellulosiruptor kristjanssonii (Calkr_0826), and Caldicellulosiruptor naganoensis (NA10_0869) were produced recombinantly in Escherichia coli and compared to Calkro_0844. All five tapirins bound to microcrystalline cellulose, switchgrass, poplar, filter paper, but not to xylan. Densitometry analysis of bound protein fractions visualized by SDS-PAGE revealed that Calhy_0908 and Calkr_0826 (from weakly cellulolytic species) associated with the cellulose substrates to a greater extent than Athe_1870, Calkro_0844 and NA10_0869 (from strongly cellulolytic species). Perhaps this relates to their specific needs to capture glucans released from lignocellulose by cellulases produced in Caldicellulosiruptor communities. Calkro_0844, and NA10_0869 share a high degree of amino acid sequence identity (> 80% identity), more so than with Athe_1870 ( approximately 50%). The amino acid sequence identities of Calhy_0908 and Calkr_0826 compared to Calkro_0844 were only 16% and 36%, respectively, although the three-dimensional structures of their C-terminal binding regions were closely related. Unlike the parent strain, C. bescii mutants lacking the tapirin genes did not bind to cellulose following short-term incubation, suggesting a role in cell association with plant biomass. Given the scarcity of carbohydrates in neutral terrestrial hot springs, tapirins likely help scavenge carbohydrates from lignocellulose to support growth and survival of Caldicellulosiruptor species.IMPORTANCE Mechanisms by which microorganisms attach to and degrade lignocellulose are important to understand if effective approaches for conversion of plant biomass into fuels and chemicals are to be developed. Caldicellulosiruptor species grow on carbohydrates from lignocellulose at elevated temperatures and have biotechnological significance for that reason. Novel cellulose binding proteins, called tapirins, are involved in the way Caldicellulosiruptor species interact with microcrystalline cellulose and here additional information about the diversity of these proteins across the genus is provided, including binding affinity and three-dimensional structural comparisons.

-	~~Authors:~~ Alahuhta, P.M., ~~Lunin, V~~.V.	+	Comparative Biochemical and Structural Analysis of Novel Cellulose Binding Proteins (Tapirins) from Extremely Thermophilic Caldicellulosiruptor Species.,Lee LL, Hart WS, Lunin VV, Alahuhta M, Bomble YJ, Himmel ME, Blumer-Schuette SE, Adams MWW, Kelly RM Appl Environ Microbiol. 2018 Nov 26. pii: AEM.01983-18. doi:, 10.1128/AEM.01983-18. PMID:30478233<ref>PMID:30478233</ref>

-	~~Description: The Crystal Structure~~ of ~~Caldicellulosiruptor kristjanssonii Tapirin C~~-~~terminal domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Lunin, V.V]]	+	<div class="pdbe-citations 6n2b" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Alahuhta, P.M~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Alahuhta, P M]]
		+	[[Category: Lunin, V V]]
		+	[[Category: Beta-helix]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Cellulose binding]]

OCA at 05:18, 12 December 2018

2018-12-12T05:18:37Z

←Older revision		Revision as of 05:18, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n2b is ON HOLD	+	The entry 6n2b is ON HOLD until Paper Publication

	Authors: Alahuhta, P.M., Lunin, V.V.		Authors: Alahuhta, P.M., Lunin, V.V.
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	Description: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain		Description: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Alahuhta, P.M]]
	[[Category: Lunin, V.V]]		[[Category: Lunin, V.V]]
		+	[[Category: Alahuhta, P.M]]

OCA: Protected "6n2b" [edit=sysop:move=sysop]

2018-12-02T19:09:05Z

Protected "6n2b" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:09, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n2b is ON HOLD Authors: Alahuhta, P.M., Lunin, V.V. Description: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal d...

2018-12-02T19:09:03Z

New page: '''Unreleased structure''' The entry 6n2b is ON HOLD Authors: Alahuhta, P.M., Lunin, V.V. Description: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal d...

New page

'''Unreleased structure'''

The entry 6n2b is ON HOLD

Authors: Alahuhta, P.M., Lunin, V.V.

Description: The Crystal Structure of Caldicellulosiruptor kristjanssonii Tapirin C-terminal domain
[[Category: Unreleased Structures]]
[[Category: Alahuhta, P.M]]
[[Category: Lunin, V.V]]