5xqj - Revision history

OCA at 08:10, 22 November 2023

OCA — Wed, 22 Nov 2023 08:10:09 GMT

←Older revision		Revision as of 08:10, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose==		==Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose==
-	<StructureSection load='5xqj' size='340' side='right' caption='[[5xqj]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='5xqj' size='340' side='right'caption='[[5xqj]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqj]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_10106 Atcc 10106~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_chrysogenum Penicillium chrysogenum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XQJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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]] 2.75Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcrglx, EN45_041150 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5076 ATCC 10106])</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=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqj OCA], [~~http~~://pdbe.org/5xqj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xqj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xqj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqj 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=5xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqj OCA], [https://pdbe.org/5xqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xqj RCSB], [https://www.ebi.ac.uk/pdbsum/5xqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B6H7Q7_PENRW B6H7Q7_PENRW]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 10106~~]]	+	[[Category: Large Structures]]
-	[[Category: Iwai, M]]	+	[[Category: Penicillium chrysogenum]]
-	[[Category: Kunishige, Y]]	+	[[Category: Iwai M]]
-	[[Category: Nishimura, S]]	+	[[Category: Kunishige Y]]
-	[[Category: Sakamoto, T]]	+	[[Category: Nishimura S]]
-	[[Category: Tada, T]]	+	[[Category: Sakamoto T]]
-	~~[[Category: Enzyme]]~~	+	[[Category: Tada T]]
-	~~[[Category: Exo-rhamnogalacturonan lyase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pectin]]~~	+
-	~~[[Category: Sad]]~~	+
-	~~[[Category: Se~~]]	+

OCA at 14:11, 11 April 2018

OCA — Wed, 11 Apr 2018 14:11:33 GMT

←Older revision		Revision as of 14:11, 11 April 2018
Line 3:		Line 3:
	<StructureSection load='5xqj' size='340' side='right' caption='[[5xqj]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5xqj' size='340' side='right' caption='[[5xqj]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xqj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xqj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_10106 Atcc 10106]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pcrglx, EN45_041150 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5076 ATCC 10106])</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=5xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqj OCA], [http://pdbe.org/5xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqj RCSB], [http://www.ebi.ac.uk/pdbsum/5xqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqj 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=5xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqj OCA], [http://pdbe.org/5xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqj RCSB], [http://www.ebi.ac.uk/pdbsum/5xqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) was recently classified as a member of polysaccharide lyase (PL) family 26 along with hypothetical proteins derived from various organisms. In this study, we determined the crystal structure of PcRGLX as the first structure of a member of this family. Based on the substrate-binding orientation and substrate specificity, PcRGLX is an exo-type PL that cleaves rhamnogalacturonan from the reducing end. Analysis of PcRGLX-complex structures with reaction products indicate that the active site possesses an L-shaped cleft that can accommodate galactosyl side chains, suggesting side-chain-bypassing activity in PcRGLX. Furthermore, we determined the residues critical for catalysis by analyzing the enzyme activities of inactive variants.
		+
		+	Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26.,Kunishige Y, Iwai M, Nakazawa M, Ueda M, Tada T, Nishimura S, Sakamoto T FEBS Lett. 2018 Mar 25. doi: 10.1002/1873-3468.13034. PMID:29574769<ref>PMID:29574769</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xqj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 10106]]
	[[Category: Iwai, M]]		[[Category: Iwai, M]]
	[[Category: Kunishige, Y]]		[[Category: Kunishige, Y]]

OCA at 05:55, 4 April 2018

OCA — Wed, 04 Apr 2018 05:55:57 GMT

←Older revision		Revision as of 05:55, 4 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5xqj is ON HOLD until Paper Publication~~	+	==Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose==
-		+	<StructureSection load='5xqj' size='340' side='right' caption='[[5xqj]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~Authors: Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xqj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XQJ FirstGlance]. <br>
-	~~Description:~~ Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5xqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xqj OCA], [http://pdbe.org/5xqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xqj RCSB], [http://www.ebi.ac.uk/pdbsum/5xqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xqj ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Tada~~, T]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Iwai, M]]		[[Category: Iwai, M]]
	[[Category: Kunishige, Y]]		[[Category: Kunishige, Y]]
		+	[[Category: Nishimura, S]]
	[[Category: Sakamoto, T]]		[[Category: Sakamoto, T]]
-	[[Category: ~~Nishimura~~, S]]	+	[[Category: Tada, T]]
		+	[[Category: Enzyme]]
		+	[[Category: Exo-rhamnogalacturonan lyase]]
		+	[[Category: Lyase]]
		+	[[Category: Pectin]]
		+	[[Category: Sad]]
		+	[[Category: Se]]

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

OCA — Wed, 27 Sep 2017 15:41:03 GMT

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

←Older revision

Revision as of 15:41, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xqj is ON HOLD until Paper Publication Authors: Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T. Description: Crystal structure of a...

OCA — Wed, 27 Sep 2017 15:41:02 GMT

New page: '''Unreleased structure''' The entry 5xqj is ON HOLD until Paper Publication Authors: Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T. Description: Crystal structure of a...

New page

'''Unreleased structure'''

The entry 5xqj is ON HOLD until Paper Publication

Authors: Kunishige, Y., Iwai, M., Tada, T., Nishimura, S., Sakamoto, T.

Description: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose
[[Category: Unreleased Structures]]
[[Category: Tada, T]]
[[Category: Iwai, M]]
[[Category: Kunishige, Y]]
[[Category: Sakamoto, T]]
[[Category: Nishimura, S]]