5ot1 - Revision history

OCA at 12:59, 20 December 2023

OCA — Wed, 20 Dec 2023 12:59:17 GMT

←Older revision		Revision as of 12:59, 20 December 2023
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	==The type III pullulan hydrolase from Thermococcus kodakarensis==		==The type III pullulan hydrolase from Thermococcus kodakarensis==
-	<StructureSection load='5ot1' size='340' side='right' caption='[[5ot1]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5ot1' size='340' side='right'caption='[[5ot1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ot1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OT1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ot1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OT1 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~~></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]] 2.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TK0977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~311400~~ "~~Thermococcus kodakaraensis~~" ~~Atomi et al. 2004])~~</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></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=5ot1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot1 OCA], [~~http~~://pdbe.org/5ot1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ot1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ot1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot1 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=5ot1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot1 OCA], [https://pdbe.org/5ot1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ot1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ot1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot1 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5JID9_THEKO Q5JID9_THEKO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Thermococcus ~~kodakaraensis atomi et al. 2004~~]]	+	[[Category: Large Structures]]
-	[[Category: Ahmad, N]]	+	[[Category: Thermococcus kodakarensis]]
-	[[Category: Akhtar, M]]	+	[[Category: Ahmad N]]
-	[[Category: Coker~~, A R~~]]	+	[[Category: Akhtar M]]
-	[[Category: Cooper~~, J B~~]]	+	[[Category: Coker AR]]
-	[[Category: Guo, J]]	+	[[Category: Cooper JB]]
-	[[Category: Keegan, R]]	+	[[Category: Guo J]]
-	[[Category: Muhammad~~, M A~~]]	+	[[Category: Keegan R]]
-	[[Category: Rashid, N]]	+	[[Category: Muhammad MA]]
-	[[Category: Wood~~, S P]]~~	+	[[Category: Rashid N]]
-	~~[[Category: Hydrolase]]~~	+	[[Category: Wood SP]]
-	~~[[Category: Thermostable]]~~	+
-	~~[[Category: Type iii pullulan hydrolase~~]]	+

OCA at 05:52, 25 April 2018

OCA — Wed, 25 Apr 2018 05:52:33 GMT

←Older revision		Revision as of 05:52, 25 April 2018
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	<StructureSection load='5ot1' size='340' side='right' caption='[[5ot1]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5ot1' size='340' side='right' caption='[[5ot1]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ot1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OT1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ot1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OT1 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK0977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 "Thermococcus kodakaraensis" Atomi et al. 2004])</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=5ot1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot1 OCA], [http://pdbe.org/5ot1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ot1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ot1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot1 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=5ot1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot1 OCA], [http://pdbe.org/5ot1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ot1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ot1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot1 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and alpha-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both alpha-1,4- and alpha-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95-100 degrees C and has a pH optimum in the range 3.5-4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 A and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine.
		+
		+	Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis.,Guo J, Coker AR, Wood SP, Cooper JB, Keegan RM, Ahmad N, Muhammad MA, Rashid N, Akhtar M Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):305-314. doi:, 10.1107/S2059798318001754. Epub 2018 Apr 3. PMID:29652257<ref>PMID:29652257</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ot1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
	[[Category: Ahmad, N]]		[[Category: Ahmad, N]]
	[[Category: Akhtar, M]]		[[Category: Akhtar, M]]

OCA at 05:37, 18 April 2018

OCA — Wed, 18 Apr 2018 05:37:20 GMT

←Older revision		Revision as of 05:37, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5ot1 is ~~ON HOLD until Paper Publication~~	+	==The type III pullulan hydrolase from Thermococcus kodakarensis==
-		+	<StructureSection load='5ot1' size='340' side='right' caption='[[5ot1]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~: ~~Guo, J~~.~~, Coker, A~~.R., ~~Wood, S~~.P., ~~Cooper~~, J.B.~~, Keegan, R~~., ~~Ahmad, N~~.~~, Muhammad, M~~.A., ~~Rashid, N~~.~~, Akhtar, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ot1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OT1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OT1 FirstGlance]. <br>
-	~~Description~~: ~~The type III pullulan hydrolase from Thermococcus kodakarensis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5ot1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ot1 OCA], [http://pdbe.org/5ot1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ot1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ot1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ot1 ProSAT]</span></td></tr>
-	[[Category: ~~Rashid~~, N]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ahmad, N]]
		+	[[Category: Akhtar, M]]
		+	[[Category: Coker, A R]]
		+	[[Category: Cooper, J B]]
	[[Category: Guo, J]]		[[Category: Guo, J]]
-	[[Category: Cooper, J.B]]
-	[[Category: Akhtar, M]]
	[[Category: Keegan, R]]		[[Category: Keegan, R]]
-	[[Category: Muhammad, M.A]]	+	[[Category: Muhammad, M A]]
-	[[Category: Wood, S.P]]	+	[[Category: Rashid, N]]
-	[[Category: ~~Ahmad, N~~]]	+	[[Category: Wood, S P]]
-	[[Category: ~~Coker, A.R~~]]	+	[[Category: Hydrolase]]
		+	[[Category: Thermostable]]
		+	[[Category: Type iii pullulan hydrolase]]

OCA: Protected "5ot1" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 12:49:15 GMT

Protected "5ot1" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:49, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ot1 is ON HOLD until Paper Publication Authors: Guo, J., Coker, A.R., Wood, S.P., Cooper, J.B., Keegan, R., Ahmad, N., Muhammad, M.A., Rashid, N., ...

OCA — Wed, 27 Sep 2017 12:49:14 GMT

New page: '''Unreleased structure''' The entry 5ot1 is ON HOLD until Paper Publication Authors: Guo, J., Coker, A.R., Wood, S.P., Cooper, J.B., Keegan, R., Ahmad, N., Muhammad, M.A., Rashid, N., ...

New page

'''Unreleased structure'''

The entry 5ot1 is ON HOLD until Paper Publication

Authors: Guo, J., Coker, A.R., Wood, S.P., Cooper, J.B., Keegan, R., Ahmad, N., Muhammad, M.A., Rashid, N., Akhtar, M.

Description: The type III pullulan hydrolase from Thermococcus kodakarensis
[[Category: Unreleased Structures]]
[[Category: Rashid, N]]
[[Category: Guo, J]]
[[Category: Cooper, J.B]]
[[Category: Akhtar, M]]
[[Category: Keegan, R]]
[[Category: Muhammad, M.A]]
[[Category: Wood, S.P]]
[[Category: Ahmad, N]]
[[Category: Coker, A.R]]