1h12 - Revision history

OCA at 11:26, 27 March 2024

OCA — Wed, 27 Mar 2024 11:26:42 GMT

←Older revision		Revision as of 11:26, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1h12' size='340' side='right'caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H12 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=XYP:BETA~~-~~D-XYLOPYRANOSE'>XYP</scene>~~, ~~<scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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]] 1.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1h13\|1h13]], [[1h14\|1h14]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8]~~ </~~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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [https://pdbe.org/1h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [https://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [https://pdbe.org/1h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [https://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8RJN8_PSEHA Q8RJN8_PSEHA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.
-
-	The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.,Van Petegem F, Collins T, Meuwis MA, Gerday C, Feller G, Van Beeumen J J Biol Chem. 2003 Feb 28;278(9):7531-9. Epub 2002 Dec 9. PMID:12475991<ref>PMID:12475991</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1h12" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Beeumen, J Van~~]]	+	[[Category: Pseudoalteromonas haloplanktis]]
-	[[Category: Collins, T]]	+	[[Category: Collins T]]
-	[[Category: Feller, G]]	+	[[Category: Feller G]]
-	[[Category: Gerday, C]]	+	[[Category: Gerday C]]
-	[[Category: Meuwis~~, M A~~]]	+	[[Category: Meuwis MA]]
-	[[Category: ~~Petegem, F~~ Van]]	+	[[Category: Van Beeumen J]]
-	[[Category: ~~Cold adaptation]]~~	+	[[Category: Van Petegem F]]
-	~~[[Category: Family 8]]~~	+
-	~~[[Category: Glycosyl hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Psychrophilic]]~~	+
-	~~[[Category: Temperature]]~~	+
-	~~[[Category: Xylan degradation~~]]	+

OCA at 09:15, 24 February 2021

OCA — Wed, 24 Feb 2021 09:15:44 GMT

←Older revision		Revision as of 09:15, 24 February 2021
Line 1:		Line 1:

-	====	+	==Structure of a cold-adapted family 8 xylanase==
-	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]]' scene=''>	+	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H12 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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [https://pdbe.org/1h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [https://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1h13\|1h13]], [[1h14\|1h14]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [https://pdbe.org/1h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [https://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.
		+
		+	The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.,Van Petegem F, Collins T, Meuwis MA, Gerday C, Feller G, Van Beeumen J J Biol Chem. 2003 Feb 28;278(9):7531-9. Epub 2002 Dec 9. PMID:12475991<ref>PMID:12475991</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1h12" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Beeumen, J Van]]
		+	[[Category: Collins, T]]
		+	[[Category: Feller, G]]
		+	[[Category: Gerday, C]]
		+	[[Category: Meuwis, M A]]
		+	[[Category: Petegem, F Van]]
		+	[[Category: Cold adaptation]]
		+	[[Category: Family 8]]
		+	[[Category: Glycosyl hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Psychrophilic]]
		+	[[Category: Temperature]]
		+	[[Category: Xylan degradation]]

OCA at 07:05, 24 February 2021

OCA — Wed, 24 Feb 2021 07:05:29 GMT

←Older revision		Revision as of 07:05, 24 February 2021
Line 1:		Line 1:

-	==~~Structure of a cold-adapted family 8 xylanase~~==	+	====
-	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]]~~, [[Resolution\|resolution]] 1.20Å~~' scene=''>	+	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=~~1H12~~ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=~~1H12~~ FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [https://pdbe.org/1h12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [https://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [~~http~~://pdbe.org/1h12 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 19:		Line 16:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.
-
-	The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.,Van Petegem F, Collins T, Meuwis MA, Gerday C, Feller G, Van Beeumen J J Biol Chem. 2003 Feb 28;278(9):7531-9. Epub 2002 Dec 9. PMID:12475991<ref>PMID:12475991</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1h12" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Beeumen, J Van]]~~	+	[[Category: Z-disk]]
-	~~[[Category: Collins, T]]~~	+
-	~~[[Category: Feller, G]]~~	+
-	~~[[Category: Gerday, C]]~~	+
-	~~[[Category: Meuwis, M A]]~~	+
-	~~[[Category: Petegem, F Van]]~~	+
-	~~[[Category: Cold adaptation]]~~	+
-	~~[[Category: Family 8]]~~	+
-	~~[[Category: Glycosyl hydrolase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Psychrophilic]]~~	+
-	~~[[Category: Temperature]]~~	+
-	~~[[Category: Xylan degradation~~]]	+

OCA at 07:17, 3 April 2019

OCA — Wed, 03 Apr 2019 07:17:06 GMT

←Older revision		Revision as of 07:17, 3 April 2019
Line 1:		Line 1:

	==Structure of a cold-adapted family 8 xylanase==		==Structure of a cold-adapted family 8 xylanase==
-	<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>	+	<StructureSection load='1h12' size='340' side='right'caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Beeumen, J Van]]		[[Category: Beeumen, J Van]]
	[[Category: Collins, T]]		[[Category: Collins, T]]

OCA at 06:13, 3 January 2018

OCA — Wed, 03 Jan 2018 06:13:46 GMT

←Older revision		Revision as of 06:13, 3 January 2018
Line 1:		Line 1:
-	==~~STRUCTURE OF A COLD~~-~~ADAPTED FAMILY~~ 8 ~~XYLANASE~~==	+
		+	==Structure of a cold-adapted family 8 xylanase==
	<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://pdbe.org/1h12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://pdbe.org/1h12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1h12 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/1h12_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/1h12_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 12:23, 8 February 2016

OCA — Mon, 08 Feb 2016 12:23:37 GMT

←Older revision		Revision as of 12:23, 8 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1h12 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:32, 10 September 2015

OCA — Thu, 10 Sep 2015 11:32:24 GMT

←Older revision		Revision as of 11:32, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"alteromonas_marinopraesens"_(zobell_and_upham_1944)_baumann_et_al._1972 "alteromonas marinopraesens" (zobell and upham 1944) baumann et al. 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://pdbe.org/1h12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1h12" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Pseudoalteromonas haloplanktis]]
	[[Category: Beeumen, J Van]]		[[Category: Beeumen, J Van]]
	[[Category: Collins, T]]		[[Category: Collins, T]]

OCA at 20:02, 22 December 2014

OCA — Mon, 22 Dec 2014 20:02:30 GMT

←Older revision		Revision as of 20:02, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 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=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Pseudoalteromonas haloplanktis]]		[[Category: Pseudoalteromonas haloplanktis]]
-	[[Category: Beeumen, J Van.]]	+	[[Category: Beeumen, J Van]]
-	[[Category: Collins, T.]]	+	[[Category: Collins, T]]
-	[[Category: Feller, G.]]	+	[[Category: Feller, G]]
-	[[Category: Gerday, C.]]	+	[[Category: Gerday, C]]
-	[[Category: Meuwis, M A.]]	+	[[Category: Meuwis, M A]]
-	[[Category: Petegem, F Van.]]	+	[[Category: Petegem, F Van]]
	[[Category: Cold adaptation]]		[[Category: Cold adaptation]]
	[[Category: Family 8]]		[[Category: Family 8]]

OCA at 09:53, 28 September 2014

OCA — Sun, 28 Sep 2014 09:53:16 GMT

←Older revision		Revision as of 09:53, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1h12.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF A COLD-ADAPTED FAMILY 8 XYLANASE==
		+	<StructureSection load='1h12' size='340' side='right' caption='[[1h12]], [[Resolution\|resolution]] 1.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1h12]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1H12 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1h13\|1h13]], [[1h14\|1h14]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h12 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1h12 RCSB], [http://www.ebi.ac.uk/pdbsum/1h12 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h1/1h12_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. The current consensus is that they have an increased flexibility, enhancing accommodation and transformation of the substrates at low energy costs. Here we describe the structure of the xylanase from the Antarctic bacterium Pseudoalteromonas haloplanktis at 1.3 A resolution. Xylanases are usually grouped into glycosyl hydrolase families 10 and 11, but this enzyme belongs to family 8. The fold differs from that of other known xylanases and can be described as an (alpha/alpha)(6) barrel. Various parameters that may explain the cold-adapted properties were examined and indicated that the protein has a reduced number of salt bridges and an increased exposure of hydrophobic residues. The crystal structures of a complex with xylobiose and of mutant D144N were obtained at 1.2 and 1.5 A resolution, respectively. Analysis of the various substrate binding sites shows that the +3 and -3 subsites are rearranged as compared to those of a family 8 homolog, while the xylobiose complex suggests the existence of a +4 subsite. A decreased acidity of the substrate binding cleft and an increased flexibility of aromatic residues lining the subsites may enhance the rate at which substrate is bound.

-	~~{{STRUCTURE_1h12\| PDB=1h12 \| SCENE= }}~~	+	The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.,Van Petegem F, Collins T, Meuwis MA, Gerday C, Feller G, Van Beeumen J J Biol Chem. 2003 Feb 28;278(9):7531-9. Epub 2002 Dec 9. PMID:12475991<ref>PMID:12475991</ref>

-	~~===STRUCTURE OF A COLD-ADAPTED FAMILY 8 XYLANASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12475991}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1h12]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudoalteromonas_haloplanktis Pseudoalteromonas haloplanktis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1H12 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012475991<~~/~~ref~~><~~ref group="xtra">PMID:015906318</ref><references group="xtra"~~/>	+
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Pseudoalteromonas haloplanktis]]		[[Category: Pseudoalteromonas haloplanktis]]

OCA: Protected "1h12" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 15:27:47 GMT

Protected "1h12" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:27, 21 November 2012