1rmg - Revision history

OCA at 08:24, 1 May 2024

OCA — Wed, 01 May 2024 08:24:59 GMT

←Older revision		Revision as of 08:24, 1 May 2024
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	<StructureSection load='1rmg' size='340' side='right'caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1rmg' size='340' side='right'caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Aspac Aspac~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [https://pdbe.org/1rmg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [https://www.ebi.ac.uk/pdbsum/1rmg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmg 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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [https://pdbe.org/1rmg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [https://www.ebi.ac.uk/pdbsum/1rmg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RHGA_ASPAC RHGA_ASPAC] Pectinolytic enzymes consist of four classes of enzymes: pectine lyase, polygalacturonase, pectin methylesterase and rhamnogalacturonase. Has a positive effect in the apple hot-mash liquefaction process. Hydrolyzes alpha-D-galacturonopyranosyl-(1,2)-alpha-L-rhamnopyranosyl linkages in the backbone of the hairy regions of pectins.<ref>PMID:9464254</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1rmg 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=1rmg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.
-
-	The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.,Petersen TN, Kauppinen S, Larsen S Structure. 1997 Apr 15;5(4):533-44. PMID:9115442<ref>PMID:9115442</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rmg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspac~~]]	+	[[Category: Aspergillus aculeatus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kauppinen, S]]	+	[[Category: Kauppinen S]]
-	[[Category: Larsen, S]]	+	[[Category: Larsen S]]
-	[[Category: Petersen~~, T N]]~~	+	[[Category: Petersen TN]]
-	~~[[Category: Glycosidase]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inverting]]~~	+
-	~~[[Category: Parallel beta-helix~~]]	+

OCA at 10:15, 15 September 2021

OCA — Wed, 15 Sep 2021 10:15:15 GMT

←Older revision		Revision as of 10:15, 15 September 2021
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	<StructureSection load='1rmg' size='340' side='right'caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1rmg' size='340' side='right'caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [~~http~~://pdbe.org/1rmg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rmg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmg 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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [https://pdbe.org/1rmg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [https://www.ebi.ac.uk/pdbsum/1rmg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 19:10, 11 December 2019

OCA — Wed, 11 Dec 2019 19:10:21 GMT

←Older revision		Revision as of 19:10, 11 December 2019
Line 1:		Line 1:

	==RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS==		==RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS==
-	<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1rmg' size='340' side='right'caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Aspac]]		[[Category: Aspac]]
		+	[[Category: Large Structures]]
	[[Category: Kauppinen, S]]		[[Category: Kauppinen, S]]
	[[Category: Larsen, S]]		[[Category: Larsen, S]]

OCA at 06:42, 8 March 2018

OCA — Thu, 08 Mar 2018 06:42:14 GMT

←Older revision		Revision as of 06:42, 8 March 2018
Line 1:		Line 1:
		+
	==RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS==		==RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS==
	<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://pdbe.org/1rmg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg 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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://pdbe.org/1rmg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rmg ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 10:		Line 11:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/1rmg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/1rmg_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>
	</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=1rmg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:31, 11 September 2015

OCA — Fri, 11 Sep 2015 07:31:39 GMT

←Older revision		Revision as of 07:31, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Aspergillus_aculeatus Aspergillus aculeatus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspac Aspac]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg 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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://pdbe.org/1rmg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 24:		Line 24:
	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 1rmg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aspergillus aculeatus~~]]	+	[[Category: Aspac]]
	[[Category: Kauppinen, S]]		[[Category: Kauppinen, S]]
	[[Category: Larsen, S]]		[[Category: Larsen, S]]

OCA at 06:45, 6 January 2015

OCA — Tue, 06 Jan 2015 06:45:34 GMT

←Older revision		Revision as of 06:45, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg 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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg 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 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Aspergillus aculeatus]]		[[Category: Aspergillus aculeatus]]
-	[[Category: Kauppinen, S.]]	+	[[Category: Kauppinen, S]]
-	[[Category: Larsen, S.]]	+	[[Category: Larsen, S]]
-	[[Category: Petersen, T N.]]	+	[[Category: Petersen, T N]]
	[[Category: Glycosidase]]		[[Category: Glycosidase]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Inverting]]		[[Category: Inverting]]
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]

OCA at 15:53, 29 September 2014

OCA — Mon, 29 Sep 2014 15:53:57 GMT

←Older revision		Revision as of 15:53, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1rmg.~~png\|left~~\|200px]]	+	==RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS==
		+	<StructureSection load='1rmg' size='340' side='right' caption='[[1rmg]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RMG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<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=1rmg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rmg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rmg RCSB], [http://www.ebi.ac.uk/pdbsum/1rmg 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/rm/1rmg_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 ==
		+	BACKGROUND: Pectic substances are the major polysaccharide components of the middle lamella and primary cell wall of dicotyledonous plants. They consist of homogalacturonan 'smooth' regions and highly rhamnified 'hairy' regions of rhamnogalacturonan. The backbone in rhamnogalacturonan-l (RG-l), which is composed of alternating galacturonic acid and rhamnose residues, is the substrate for a new class of enzymes known as rhamnogalacturnoases (RGases). RGase A is a novel enzyme implicated in the enzymatic degradation of RG-l. RESULTS: The structure of RGase A from Aspergillus aculeatus has been solved by the single isomorphous replacement method including anomalous scattering (SIRAS method) to 2.0 A resolution. The enzyme folds into a large right-handed parallel beta helix, with a core composed of 13 turns of beta strands. Four parallel beta sheets (PB1, PB1a, PB2 and PB3), formed by the consecutive turns, are typically separated by a residue in the conformation of a left-handed alpha helix. As a consequence of the consecutive turns, 32% of all residues have their sidechains aligned at the surface or in the interior of the parallel beta helix. The aligned residues at the surface are dominated by threonine, aspartic acid and asparagine, whereas valine, leucine and isoleucine are most frequently found in the interior. A very large hydrophobic cavity is found in the interior of the parallel beta helix. The potential active site is a groove, oriented almost perpendicular to the helical axis, containing a cluster of three aspartic acid residues and one glutamic acid residue. The enzyme is highly glycosylated; two N-linked and eighteen O-linked glycosylation sites have been found in the structure. CONCLUSIONS: Rhamnogalacturonase A from A. aculeatus is the first three-dimensional structure of an enzyme hydrolyzing glycoside bonds within the backbone of RG-l. The large groove, which is the potential active site of RGase A, is also seen in the structures of pectate lyases. Two catalytic aspartic acid residues, which have been proposed to have a catalytic role, reside in this area of RGase A. The distance between the aspartic acid residues is consistent with the inverting mechanism of catalysis. The glycan groups bound to RGase A are important to the stability of the crystal, as the carbohydrate moiety is involved in most of the intermolecular hydrogen bonds.

-	~~{{STRUCTURE_1rmg\| PDB=1rmg \| SCENE= }}~~	+	The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix.,Petersen TN, Kauppinen S, Larsen S Structure. 1997 Apr 15;5(4):533-44. PMID:9115442<ref>PMID:9115442</ref>

-	~~===RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9115442}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1rmg]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009115442<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aspergillus aculeatus]]		[[Category: Aspergillus aculeatus]]
	[[Category: Kauppinen, S.]]		[[Category: Kauppinen, S.]]

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

OCA — Fri, 04 Jan 2013 10:06:53 GMT

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

←Older revision

Revision as of 10:06, 4 January 2013

OCA at 10:06, 4 January 2013

OCA — Fri, 04 Jan 2013 10:06:51 GMT

←Older revision		Revision as of 10:06, 4 January 2013
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-	{{Seed}}
	[[Image:1rmg.png\|left\|200px]]		[[Image:1rmg.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rmg", 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_1rmg\| PDB=1rmg \| SCENE= }}		{{STRUCTURE_1rmg\| PDB=1rmg \| SCENE= }}

	===RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS===		===RHAMNOGALACTURONASE A FROM ASPERGILLUS ACULEATUS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9115442}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9115442 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9115442}}		{{ABSTRACT_PUBMED_9115442}}

	==About this Structure==		==About this Structure==
-	~~1RMG~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA].	+	[[1rmg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9115442~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009115442</ref><references group="xtra"/>
	[[Category: Aspergillus aculeatus]]		[[Category: Aspergillus aculeatus]]
	[[Category: Kauppinen, S.]]		[[Category: Kauppinen, S.]]
Line 32:		Line 20:
	[[Category: Inverting]]		[[Category: Inverting]]
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:10:33 2009''

OCA at 15:10, 17 February 2009

OCA — Tue, 17 Feb 2009 15:10:34 GMT

←Older revision		Revision as of 15:10, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1RMG is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA].	+	1RMG is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_aculeatus Aspergillus aculeatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RMG OCA].

	==Reference==		==Reference==
-	~~The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix., Petersen TN, Kauppinen S, Larsen S, Structure. 1997 Apr 15;5(4):533-44.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/9115442 9115442]~~	+	<ref group="xtra">PMID:9115442</ref><references group="xtra"/>
	[[Category: Aspergillus aculeatus]]		[[Category: Aspergillus aculeatus]]
-	[[Category: Single protein]]
	[[Category: Kauppinen, S.]]		[[Category: Kauppinen, S.]]
	[[Category: Larsen, S.]]		[[Category: Larsen, S.]]
Line 34:		Line 33:
	[[Category: Parallel beta-helix]]		[[Category: Parallel beta-helix]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 00~~:02:~~24 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:10:33 2009''