7zei - Revision history

OCA at 07:55, 1 May 2024

OCA — Wed, 01 May 2024 07:55:19 GMT

←Older revision		Revision as of 07:55, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7zei]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldicellulosiruptor_hydrothermalis Caldicellulosiruptor hydrothermalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEI FirstGlance]. <br>		<table><tr><td colspan='2'>[[7zei]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldicellulosiruptor_hydrothermalis Caldicellulosiruptor hydrothermalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEI FirstGlance]. <br>
-	</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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.7Å</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>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=7zei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zei OCA], [https://pdbe.org/7zei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zei RCSB], [https://www.ebi.ac.uk/pdbsum/7zei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zei 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=7zei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zei OCA], [https://pdbe.org/7zei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zei RCSB], [https://www.ebi.ac.uk/pdbsum/7zei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zei ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/E4QB49_CALH1 E4QB49_CALH1]]	+	[https://www.uniprot.org/uniprot/E4QB49_CALH1 E4QB49_CALH1]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on beta-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated-Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A-cleaved pNP-alpha-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the alpha-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A(3)X, A(2,3)XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed beta-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.	+
-		+
-	Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting alpha-L-Arabinofuranosidase Activity.,Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W Front Mol Biosci. 2022 Jun 29;9:907439. doi: 10.3389/fmolb.2022.907439., eCollection 2022. PMID:35847984<ref>PMID:35847984</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7zei" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 03:25, 8 September 2022

OCA — Thu, 08 Sep 2022 03:25:12 GMT

←Older revision		Revision as of 03:25, 8 September 2022
Line 1:		Line 1:

	==Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A==		==Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A==
-	<StructureSection load='7zei' size='340' side='right'caption='[[7zei]]' scene=''>	+	<StructureSection load='7zei' size='340' side='right'caption='[[7zei]], [[Resolution\|resolution]] 1.70Å' 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=7ZEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7zei]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldicellulosiruptor_hydrothermalis Caldicellulosiruptor hydrothermalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEI 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=7zei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zei OCA], [https://pdbe.org/7zei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zei RCSB], [https://www.ebi.ac.uk/pdbsum/7zei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zei 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=7zei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zei OCA], [https://pdbe.org/7zei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zei RCSB], [https://www.ebi.ac.uk/pdbsum/7zei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zei ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/E4QB49_CALH1 E4QB49_CALH1]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on beta-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated-Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A-cleaved pNP-alpha-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the alpha-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A(3)X, A(2,3)XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed beta-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
		+
		+	Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting alpha-L-Arabinofuranosidase Activity.,Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W Front Mol Biosci. 2022 Jun 29;9:907439. doi: 10.3389/fmolb.2022.907439., eCollection 2022. PMID:35847984<ref>PMID:35847984</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7zei" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Caldicellulosiruptor hydrothermalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Baudrexl M]]		[[Category: Baudrexl M]]

OCA at 04:55, 3 August 2022

OCA — Wed, 03 Aug 2022 04:55:36 GMT

←Older revision		Revision as of 04:55, 3 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7zei ~~is ON HOLD until Paper Publication~~	+	==Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A==
-		+	<StructureSection load='7zei' size='340' side='right'caption='[[7zei]]' scene=''>
-	~~Authors~~: ~~Baudrexl, M~~.~~, Fida, T~~., ~~Berk, B~~., ~~Schwarz, W~~., ~~Zverlov, V~~.V., ~~Groll, M~~., ~~Liebl, W~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ZEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZEI FirstGlance]. <br>
-	~~Description: Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A~~	+	</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=7zei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zei OCA], [https://pdbe.org/7zei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zei RCSB], [https://www.ebi.ac.uk/pdbsum/7zei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zei ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Baudrexl, M]]	+	__TOC__
-	[[Category: ~~Liebl, W~~]]	+	</StructureSection>
-	[[Category: ~~Zverlov, V.V~~]]	+	[[Category: Large Structures]]
-	[[Category: Groll, M]]	+	[[Category: Baudrexl M]]
-	[[Category: ~~Schwarz,~~ W]]	+	[[Category: Berk B]]
-	[[Category: ~~Fida, T~~]]	+	[[Category: Fida T]]
-	[[Category: ~~Berk, B~~]]	+	[[Category: Groll M]]
		+	[[Category: Liebl W]]
		+	[[Category: Schwarz W]]
		+	[[Category: Zverlov VV]]

OCA at 08:46, 13 April 2022

OCA — Wed, 13 Apr 2022 08:46:36 GMT

←Older revision		Revision as of 08:46, 13 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7zei is ON HOLD	+	The entry 7zei is ON HOLD until Paper Publication

	Authors: Baudrexl, M., Fida, T., Berk, B., Schwarz, W., Zverlov, V.V., Groll, M., Liebl, W.		Authors: Baudrexl, M., Fida, T., Berk, B., Schwarz, W., Zverlov, V.V., Groll, M., Liebl, W.

OCA: Protected "7zei" [edit=sysop:move=sysop]

OCA — Wed, 06 Apr 2022 09:26:04 GMT

Protected "7zei" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:26, 6 April 2022

OCA: New page: '''Unreleased structure''' The entry 7zei is ON HOLD Authors: Baudrexl, M., Fida, T., Berk, B., Schwarz, W., Zverlov, V.V., Groll, M., Liebl, W. Description: Thermostable GH159 glycosi...

OCA — Wed, 06 Apr 2022 09:26:03 GMT

New page: '''Unreleased structure''' The entry 7zei is ON HOLD Authors: Baudrexl, M., Fida, T., Berk, B., Schwarz, W., Zverlov, V.V., Groll, M., Liebl, W. Description: Thermostable GH159 glycosi...

New page

'''Unreleased structure'''

The entry 7zei is ON HOLD

Authors: Baudrexl, M., Fida, T., Berk, B., Schwarz, W., Zverlov, V.V., Groll, M., Liebl, W.

Description: Thermostable GH159 glycoside hydrolase from Caldicellulosiruptor at 1.7 A
[[Category: Unreleased Structures]]
[[Category: Baudrexl, M]]
[[Category: Liebl, W]]
[[Category: Zverlov, V.V]]
[[Category: Groll, M]]
[[Category: Schwarz, W]]
[[Category: Fida, T]]
[[Category: Berk, B]]