3n92 - Revision history

OCA at 09:11, 6 September 2023

2023-09-06T09:11:12Z

←Older revision		Revision as of 09:11, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3n92' size='340' side='right'caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>		<StructureSection load='3n92' size='340' side='right'caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3n92]] is a 1 chain structure with sequence from [https://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=3N92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3n92]] 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=3N92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N92 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BGC:BETA~~-~~D-GLUCOSE'>BGC</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]] 2.89Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3n8t\|3n8t]], [[3n98\|3n98]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TK1436 ([https://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~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18]~~ </~~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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [https://pdbe.org/3n92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [https://www.ebi.ac.uk/pdbsum/3n92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n92 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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [https://pdbe.org/3n92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [https://www.ebi.ac.uk/pdbsum/3n92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n92 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BE_THEKO BE_THEKO]] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>	+	[https://www.uniprot.org/uniprot/BE_THEKO BE_THEKO] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
-	[[Category: 1,4-alpha-glucan branching enzyme]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arni~~, R K~~]]	+	[[Category: Thermococcus kodakarensis]]
-	[[Category: Betzel, C]]	+	[[Category: Arni RK]]
-	[[Category: Imanaka, T]]	+	[[Category: Betzel C]]
-	[[Category: Kanai, T]]	+	[[Category: Imanaka T]]
-	[[Category: Kuriki, T]]	+	[[Category: Kanai T]]
-	[[Category: Murakami~~, M T~~]]	+	[[Category: Kuriki T]]
-	[[Category: Santos~~, C R~~]]	+	[[Category: Murakami MT]]
-	[[Category: Takata, H]]	+	[[Category: Santos CR]]
-	[[Category: Tonoli~~, C C.C~~]]	+	[[Category: Takata H]]
-	[[Category: Trindade~~, D M]]~~	+	[[Category: Tonoli CCC]]
-	~~[[Category: Branching enzyme]]~~	+	[[Category: Trindade DM]]
-	~~[[Category: Gh57 family member]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 06:57, 12 May 2022

2022-05-12T06:57:34Z

←Older revision		Revision as of 06:57, 12 May 2022
Line 1:		Line 1:

	==Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose==		==Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose==
-	<StructureSection load='3n92' size='340' side='right' caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>	+	<StructureSection load='3n92' size='340' side='right'caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3n92]] 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=3N92 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3N92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3n92]] is a 1 chain structure with sequence from [https://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=3N92 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N92 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n8t\|3n8t]], [[3n98\|3n98]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3n8t\|3n8t]], [[3n98\|3n98]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1436 ([~~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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1436 ([https://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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [~~http~~://pdbe.org/3n92 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3n92 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3n92 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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [https://pdbe.org/3n92 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [https://www.ebi.ac.uk/pdbsum/3n92 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n92 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BE_THEKO BE_THEKO]] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>	+	[[https://www.uniprot.org/uniprot/BE_THEKO BE_THEKO]] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==See Also==		==See Also==
-	*[[Amylase\|Amylase]]	+	*[[Amylase 3D structures\|Amylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]		[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
	[[Category: 1,4-alpha-glucan branching enzyme]]		[[Category: 1,4-alpha-glucan branching enzyme]]
		+	[[Category: Large Structures]]
	[[Category: Arni, R K]]		[[Category: Arni, R K]]
	[[Category: Betzel, C]]		[[Category: Betzel, C]]

OCA at 13:06, 16 January 2019

2019-01-16T13:06:40Z

←Older revision		Revision as of 13:06, 16 January 2019
Line 24:		Line 24:
	==See Also==		==See Also==
	*[[Amylase\|Amylase]]		*[[Amylase\|Amylase]]
-	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:58, 10 December 2016

2016-12-10T03:58:18Z

←Older revision		Revision as of 03:58, 10 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose==		==Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose==
	<StructureSection load='3n92' size='340' side='right' caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>		<StructureSection load='3n92' size='340' side='right' caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3n92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermococcus_kodakarensis Thermococcus kodakarensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N92 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3n92]] 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=3N92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N92 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n8t\|3n8t]], [[3n98\|3n98]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n8t\|3n8t]], [[3n98\|3n98]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1436 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 Thermococcus ~~kodakarensis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1436 ([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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [http://www.ebi.ac.uk/pdbsum/3n92 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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [http://pdbe.org/3n92 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [http://www.ebi.ac.uk/pdbsum/3n92 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3n92 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BE_THEKO BE_THEKO]] Catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. The branch chain-length distribution of the reaction products shows degree of polymerization (DP) of 5 to 30, with two local maxima at DP 6 and DP 11. Exhibits an alpha-retaining catalytic mechanism. Does not display alpha-galactosidase or pullulanase activity, since melibiose and pullulan are not substrates. Is not able to catalyze the hydrolysis or transglycosylation of maltoheptaose, suggesting that the TK1436 protein contains neither alpha-amylase nor 4-alpha-glucanotransferase activity.<ref>PMID:16885460</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 20:
	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 3n92" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
	[[Category: 1,4-alpha-glucan branching enzyme]]		[[Category: 1,4-alpha-glucan branching enzyme]]
-	[[Category: Thermococcus kodakarensis]]
	[[Category: Arni, R K]]		[[Category: Arni, R K]]
	[[Category: Betzel, C]]		[[Category: Betzel, C]]

OCA at 08:53, 9 December 2014

2014-12-09T08:53:58Z

←Older revision		Revision as of 08:53, 9 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3n92.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose==
		+	<StructureSection load='3n92' size='340' side='right' caption='[[3n92]], [[Resolution\|resolution]] 2.89Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3n92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N92 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n8t\|3n8t]], [[3n98\|3n98]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TK1436 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311400 Thermococcus kodakarensis])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1,4-alpha-glucan_branching_enzyme 1,4-alpha-glucan branching enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.18 2.4.1.18] </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=3n92 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n92 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n92 RCSB], [http://www.ebi.ac.uk/pdbsum/3n92 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Branching enzymes (BEs) catalyze the formation of branch points in glycogen and amylopectin by cleavage of alpha-1,4 glycosidic bonds and subsequent transfer to a new alpha-1,6 position. BEs generally belong to glycoside hydrolase family 13 (GH13); however TK1436, isolated from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, is the first GH57 member, which possesses BE activity. To date, the only BE structure that had been determined is a GH13-type from Escherichia coli. Herein, we have determined the crystal structure of TK1436 in the native state and in complex with glucose and substrate mimetics that permitted mapping of the substrate-binding channel and identification of key residues for glucanotransferase activity. Its structure encompasses a distorted (beta/alpha)(7)-barrel juxtaposed to a C-terminal alpha-helical domain, which also participates in the formation of the active-site cleft. The active site comprises two acidic catalytic residues (Glu183 and Asp354), the polarizer His10, aromatic gate-keepers (Trp28, Trp270, Trp407, and Trp416) and the residue Tyr233, which is fully conserved among GH13- and GH57-type BEs. Despite TK1436 displaying a completely different fold and domain organization when compared to E. coli BE, they share the same structural determinants for BE activity. Structural comparison with AmyC, a GH57 alpha-amylase devoid of BE activity, revealed that the catalytic loop involved in substrate recognition and binding, is shortened in AmyC structure and it has been addressed as a key feature for its inability for glucanotransferase activity. The oligomerization has also been pointed out as a possible determinant for functional differentiation among GH57 members.

-	~~{{STRUCTURE_3n92\| PDB=3n92 \| SCENE= }}~~	+	Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.,Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, Murakami MT Proteins. 2011 Feb;79(2):547-57. PMID:21104698<ref>PMID:21104698</ref>

-	~~===Crystal structure of TK1436~~, a ~~GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_21104698}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3n92]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].~~	+

	==See Also==		==See Also==
-	*[[~~Alpha-~~Amylase\|~~Alpha-~~Amylase]]	+	*[[Amylase\|Amylase]]
-		+	*[[User:Gabriel Pons/Sandbox 2\|User:Gabriel Pons/Sandbox 2]]
-	==~~Reference~~==	+	== References ==
-	<~~ref group="xtra">PMID:021104698<~~/~~ref~~><~~references group="xtra"~~/>	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: 1,4-alpha-glucan branching enzyme]]		[[Category: 1,4-alpha-glucan branching enzyme]]
	[[Category: Thermococcus kodakarensis]]		[[Category: Thermococcus kodakarensis]]
-	[[Category: Arni, R K.]]	+	[[Category: Arni, R K]]
-	[[Category: Betzel, C.]]	+	[[Category: Betzel, C]]
-	[[Category: Imanaka, T.]]	+	[[Category: Imanaka, T]]
-	[[Category: Kanai, T.]]	+	[[Category: Kanai, T]]
-	[[Category: Kuriki, T.]]	+	[[Category: Kuriki, T]]
-	[[Category: Murakami, M T.]]	+	[[Category: Murakami, M T]]
-	[[Category: Santos, C R.]]	+	[[Category: Santos, C R]]
-	[[Category: Takata, H.]]	+	[[Category: Takata, H]]
-	[[Category: Tonoli, C C.C.]]	+	[[Category: Tonoli, C C.C]]
-	[[Category: Trindade, D M.]]	+	[[Category: Trindade, D M]]
	[[Category: Branching enzyme]]		[[Category: Branching enzyme]]
	[[Category: Gh57 family member]]		[[Category: Gh57 family member]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:22, 20 October 2012

2012-10-20T09:22:59Z

←Older revision		Revision as of 09:22, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3n92]] is a 1 chain structure ~~of [[Alpha-Amylase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].	+	[[3n92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].

	==See Also==		==See Also==

OCA at 22:40, 25 July 2012

2012-07-25T22:40:17Z

←Older revision		Revision as of 22:40, 25 July 2012
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	[[Image:3n92.png\|left\|200px]]		[[Image:3n92.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3n92", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3n92\| PDB=3n92 \| SCENE= }}		{{STRUCTURE_3n92\| PDB=3n92 \| SCENE= }}

	===Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===		===Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_21104698}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 21104698 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_21104698}}		{{ABSTRACT_PUBMED_21104698}}

	==About this Structure==		==About this Structure==
-	[[3n92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].	+	[[3n92]] is a 1 chain structure of [[Alpha-Amylase]] with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].
		+
		+	==See Also==
		+	*[[Alpha-Amylase\|Alpha-Amylase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21104698~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021104698</ref><references group="xtra"/>
	[[Category: 1,4-alpha-glucan branching enzyme]]		[[Category: 1,4-alpha-glucan branching enzyme]]
	[[Category: Thermococcus kodakarensis]]		[[Category: Thermococcus kodakarensis]]
Line 35:		Line 27:
	[[Category: Tonoli, C C.C.]]		[[Category: Tonoli, C C.C.]]
	[[Category: Trindade, D M.]]		[[Category: Trindade, D M.]]
		+	[[Category: Branching enzyme]]
		+	[[Category: Gh57 family member]]
		+	[[Category: Transferase]]

OCA: Protected "3n92" [edit=sysop:move=sysop]

2011-01-26T12:32:21Z

Protected "3n92" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:32, 26 January 2011

OCA at 12:32, 26 January 2011

2011-01-26T12:32:20Z

←Older revision		Revision as of 12:32, 26 January 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3n92.png\|left\|200px]]
-	[[Image:3n92.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	===Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===		===Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21104698}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21104698 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21104698}}

	==About this Structure==		==About this Structure==
-	~~3N92~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].	+	[[3n92]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21104698</ref><references group="xtra"/>
	[[Category: 1,4-alpha-glucan branching enzyme]]		[[Category: 1,4-alpha-glucan branching enzyme]]
	[[Category: Thermococcus kodakarensis]]		[[Category: Thermococcus kodakarensis]]
Line 27:		Line 35:
	[[Category: Tonoli, C C.C.]]		[[Category: Tonoli, C C.C.]]
	[[Category: Trindade, D M.]]		[[Category: Trindade, D M.]]
-	[[Category: Branching enzyme]]
-	[[Category: Gh57 family member]]
-	[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 12:12:17 2010''

OCA at 09:01, 27 October 2010

2010-10-27T09:01:55Z

←Older revision		Revision as of 09:01, 27 October 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3n92.jpg\|left\|200px]]

-	The ~~entry 3n92~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3n92", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3n92\| PDB=3n92 \| SCENE= }}

-	~~Authors: Santos~~, ~~C.R.~~, ~~Tonoli, C.C.C., Trindade, D.M., Betzel, C., Takata, H., Kuriki, T., Kanai, T., Imanaka, T., Arni, R.K., Murakami, M.T.~~	+	===Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose===

-	Description: Crystal structure of TK1436, a GH57 branching enzyme from hyperthermophilic archaeon Thermococcus kodakaraensis, in complex with glucose

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 16 08~~:29:29 2010''	+	==About this Structure==
		+	3N92 is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N92 OCA].
		+	[[Category: 1,4-alpha-glucan branching enzyme]]
		+	[[Category: Thermococcus kodakarensis]]
		+	[[Category: Arni, R K.]]
		+	[[Category: Betzel, C.]]
		+	[[Category: Imanaka, T.]]
		+	[[Category: Kanai, T.]]
		+	[[Category: Kuriki, T.]]
		+	[[Category: Murakami, M T.]]
		+	[[Category: Santos, C R.]]
		+	[[Category: Takata, H.]]
		+	[[Category: Tonoli, C C.C.]]
		+	[[Category: Trindade, D M.]]
		+	[[Category: Branching enzyme]]
		+	[[Category: Gh57 family member]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 27 12:12:17 2010''