5ocr - Revision history

OCA at 09:40, 6 December 2023

2023-12-06T09:40:18Z

← Older revision		Revision as of 09:40, 6 December 2023
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	==Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans==		==Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans==
	<StructureSection load='5ocr' size='340' side='right' caption='[[5ocr]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='5ocr' size='340' side='right'caption='[[5ocr]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ocr]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"cytophaga_drobachiensis"_barbeyron_et_al._1998 "cytophaga drobachiensis" barbeyron et al. 1998~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OCR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OCR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ocr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OCR FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.66Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>cgkA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~63186~~ "~~Cytophaga drobachiensis~~" ~~Barbeyron et al. 1998])</td~~><~~/tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83]~~ </~~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=5ocr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ocr OCA], [https://pdbe.org/5ocr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ocr RCSB], [https://www.ebi.ac.uk/pdbsum/5ocr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ocr 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=5ocr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ocr OCA], [~~http~~://pdbe.org/5ocr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ocr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ocr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ocr ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/G0L921_ZOBGA G0L921_ZOBGA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Cytophaga drobachiensis barbeyron et al. 1998~~]]		[[Category: Large Structures]]
	[[Category: ~~Kappa-carrageenase~~]]		[[Category: Zobellia galactanivorans]]
	[[Category: Czjzek, M]]		[[Category: Czjzek M]]
	[[Category: Jeudy, A]]		[[Category: Jeudy A]]
	[[Category: Larocque, R]]		[[Category: Larocque R]]
	[[Category: Matard-Mann, M]]		[[Category: Matard-Mann M]]
	[[Category: Michel, G]]		[[Category: Michel G]]
	~~[[Category: Beta-jellyroll]]~~
	~~[[Category: Glycoside hydrolase 16]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Marine polysaccharidase~~]]

OCA at 07:44, 6 December 2017

2017-12-06T07:44:17Z

← Older revision		Revision as of 07:44, 6 December 2017
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	<StructureSection load='5ocr' size='340' side='right' caption='[[5ocr]], [[Resolution\|resolution]] 1.66Å' scene=''>		<StructureSection load='5ocr' size='340' side='right' caption='[[5ocr]], [[Resolution\|resolution]] 1.66Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ocr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OCR FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ocr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"cytophaga_drobachiensis"_barbeyron_et_al._1998 "cytophaga drobachiensis" barbeyron et al. 1998]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OCR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cgkA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63186 "Cytophaga drobachiensis" Barbeyron et al. 1998])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83] </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=5ocr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ocr OCA], [http://pdbe.org/5ocr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ocr RCSB], [http://www.ebi.ac.uk/pdbsum/5ocr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ocr 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=5ocr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ocr OCA], [http://pdbe.org/5ocr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ocr RCSB], [http://www.ebi.ac.uk/pdbsum/5ocr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ocr ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Carrageenans are sulfated alpha-1,3-beta-1,4-galactans found in the cell wall of some red algae that are practically valuable for their gelation and biomimetic properties but also serve as a potential carbon source for marine bacteria. Carbohydrate degradation has been studied extensively for terrestrial plant/bacterial systems, but sulfation is not present in these cases, meaning the marine enzymes used to degrade carrageenans must possess unique features to recognize these modifications. To gain insights into these features, we have focused on kappa-carrageenases from two distant bacterial phyla, which belong to glycoside hydrolase family 16 and cleave the beta-1,4 linkage of kappa-carrageenan. We have solved the crystal structure of the catalytic module of ZgCgkA from Zobellia galactanivorans at 1.66 A resolution and compared it with the only other structure available, that of PcCgkA from Pseudoalteromonas carrageenovora 9(T) (ATCC 43555(T)). We also describe the first substrate complex in the inactivated mutant form of PcCgkA at 1.7 A resolution. The structural and biochemical comparison of these enzymes suggests key determinants that underlie the functional properties of this subfamily. In particular, we identified several arginine residues that interact with the polyanionic substrate, and confirmed the functional relevance of these amino acids using a targeted mutagenesis strategy. These results give new insight into the diversity of the kappa-carrageenase subfamily. The phylogenetic analyses show the presence of several distinct clades of enzymes that relate to differences in modes of action or subtle differences within the same substrate specificity, matching the hybrid character of the kappa-carrageenan polymer.

			Structural insights into marine carbohydrate degradation by family GH16 kappa-carrageenases.,Matard-Mann M, Bernard T, Leroux C, Barbeyron T, Larocque R, Prechoux A, Jeudy A, Jam M, Nyvall Collen P, Michel G, Czjzek M J Biol Chem. 2017 Dec 1;292(48):19919-19934. doi: 10.1074/jbc.M117.808279. Epub, 2017 Oct 13. PMID:29030427<ref>PMID:29030427</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5ocr" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Cytophaga drobachiensis barbeyron et al. 1998]]
	[[Category: Kappa-carrageenase]]		[[Category: Kappa-carrageenase]]
	[[Category: Czjzek, M]]		[[Category: Czjzek, M]]

OCA at 07:11, 18 October 2017

2017-10-18T07:11:16Z

← Older revision		Revision as of 07:11, 18 October 2017
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	~~'''Unreleased structure'''~~

	~~The entry~~ 5ocr is ~~ON HOLD~~		==Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans==
			<StructureSection load='5ocr' size='340' side='right' caption='[[5ocr]], [[Resolution\|resolution]] 1.66Å' scene=''>
	~~Authors~~: ~~Czjzek~~, M., ~~Matard~~-~~Mann~~, M., ~~Michel~~, G., ~~Jeudy, A~~.~~, Larocque, R~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5ocr]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OCR FirstGlance]. <br>
	~~Description: Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Kappa-carrageenase Kappa-carrageenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.83 3.2.1.83] </span></td></tr>
	[[Category: ~~Michel~~, G]]		<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=5ocr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ocr OCA], [http://pdbe.org/5ocr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ocr RCSB], [http://www.ebi.ac.uk/pdbsum/5ocr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ocr ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Kappa-carrageenase]]
			[[Category: Czjzek, M]]
	[[Category: Jeudy, A]]		[[Category: Jeudy, A]]
	[[Category: ~~Czjzek~~, M]]		[[Category: Larocque, R]]
	[[Category: Matard-Mann, M]]		[[Category: Matard-Mann, M]]
	[[Category: ~~Larocque~~, R]]		[[Category: Michel, G]]
			[[Category: Beta-jellyroll]]
			[[Category: Glycoside hydrolase 16]]
			[[Category: Hydrolase]]
			[[Category: Marine polysaccharidase]]

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

2017-09-27T12:17:09Z

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

← Older revision	Revision as of 12:17, 27 September 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5ocr is ON HOLD Authors: Czjzek, M., Matard-Mann, M., Michel, G., Jeudy, A., Larocque, R. Description: Crystal structure of the kappa-carrageenase ...

2017-09-27T12:17:08Z

New page: '''Unreleased structure''' The entry 5ocr is ON HOLD Authors: Czjzek, M., Matard-Mann, M., Michel, G., Jeudy, A., Larocque, R. Description: Crystal structure of the kappa-carrageenase ...

New page

'''Unreleased structure'''

The entry 5ocr is ON HOLD

Authors: Czjzek, M., Matard-Mann, M., Michel, G., Jeudy, A., Larocque, R.

Description: Crystal structure of the kappa-carrageenase zobellia_236 from Zobellia galactanivorans
[[Category: Unreleased Structures]]
[[Category: Michel, G]]
[[Category: Jeudy, A]]
[[Category: Czjzek, M]]
[[Category: Matard-Mann, M]]
[[Category: Larocque, R]]