1nkg

From Proteopedia

(Difference between revisions)

Current revision

Rhamnogalacturonan lyase from Aspergillus aculeatus

Structural highlights

1nkg is a 1 chain structure with sequence from Aspergillus aculeatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RGLA_ASPAC Pectinolytic enzyme that has a positive effect in the apple hot-mash liquefaction process. This endolyase hydrolyzes the alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galacturonopyranosyl glycosidic linkage by beta-elimination, thereby generating oligosaccharides terminating at the non-reducing end with a hex-4-enopyranosyluronic acid residue.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Rhamnogalacturonan lyase (RG-lyase) specifically recognizes and cleaves alpha-1,4 glycosidic bonds between L-rhamnose and D-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. The three-dimensional structure of RG-lyase from Aspergillus aculeatus has been determined to 1.5 A resolution representing the first known structure from polysaccharide lyase family 4 and of an enzyme with this catalytic specificity. The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows structural homology to non-catalytic domains from other carbohydrate active enzymes.

Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4.,McDonough MA, Kadirvelraj R, Harris P, Poulsen JC, Larsen S FEBS Lett. 2004 May 7;565(1-3):188-94. PMID:15135077^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL. Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus. J Mol Biol. 2010 Sep 17. PMID:20851126 doi:10.1016/j.jmb.2010.09.013
↑ Mutter M, Colquhoun IJ, Schols HA, Beldman G, Voragen AG. Rhamnogalacturonase B from Aspergillus aculeatus is a rhamnogalacturonan alpha-L-rhamnopyranosyl-(1-->4)-alpha-D-galactopyranosyluronide lyase. Plant Physiol. 1996 Jan;110(1):73-7. PMID:8587995
↑ Mutter M, Colquhoun IJ, Beldman G, Schols HA, Bakx EJ, Voragen AG. Characterization of recombinant rhamnogalacturonan alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galactopyranosyluronide lyase from Aspergillus aculeatus. An enzyme that fragments rhamnogalacturonan I regions of pectin. Plant Physiol. 1998 May;117(1):141-52. PMID:9576783
↑ McDonough MA, Kadirvelraj R, Harris P, Poulsen JC, Larsen S. Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4. FEBS Lett. 2004 May 7;565(1-3):188-94. PMID:15135077 doi:10.1016/j.febslet.2004.03.094

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nkg"

@@ Line 1: / Line 1: @@
 ==Rhamnogalacturonan lyase from Aspergillus aculeatus==
-<StructureSection load='1nkg' size='340' side='right' caption='[[1nkg]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='1nkg' size='340' side='right'caption='[[1nkg]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nkg]] 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=1NKG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NKG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1nkg]] 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=1NKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKG 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=SO4:SULFATE+ION'>SO4</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]] 1.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RHGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5053 ASPAC])</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=SO4:SULFATE+ION'>SO4</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=1nkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkg OCA], [http://pdbe.org/1nkg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nkg RCSB], [http://www.ebi.ac.uk/pdbsum/1nkg PDBsum]</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=1nkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkg OCA], [https://pdbe.org/1nkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkg RCSB], [https://www.ebi.ac.uk/pdbsum/1nkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RGLA_ASPAC RGLA_ASPAC]] Pectinolytic enzyme that has a positive effect in the apple hot-mash liquefaction process. This endolyase hydrolyzes the alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galacturonopyranosyl glycosidic linkage by beta-elimination, thereby generating oligosaccharides terminating at the non-reducing end with a hex-4-enopyranosyluronic acid residue.<ref>PMID:20851126</ref> <ref>PMID:8587995</ref> <ref>PMID:9576783</ref>
+[https://www.uniprot.org/uniprot/RGLA_ASPAC RGLA_ASPAC] Pectinolytic enzyme that has a positive effect in the apple hot-mash liquefaction process. This endolyase hydrolyzes the alpha-L-rhamnopyranosyl-(1,4)-alpha-D-galacturonopyranosyl glycosidic linkage by beta-elimination, thereby generating oligosaccharides terminating at the non-reducing end with a hex-4-enopyranosyluronic acid residue.<ref>PMID:20851126</ref> <ref>PMID:8587995</ref> <ref>PMID:9576783</ref>
 == 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/nk/1nkg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkg_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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].
+</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=1nkg ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Aspac]]
+[[Category: Aspergillus aculeatus]]
-[[Category: Harris, P]]
+[[Category: Large Structures]]
-[[Category: Kadirvelraj, R]]
+[[Category: Harris P]]
-[[Category: Larsen, S]]
+[[Category: Kadirvelraj R]]
-[[Category: McDonough, M A]]
+[[Category: Larsen S]]
-[[Category: Poulsen, J C]]
+[[Category: McDonough MA]]
-[[Category: Carbohydrate active enzyme]]
+[[Category: Poulsen JC]]
-[[Category: Lyase]]
-[[Category: Pectin]]
-[[Category: Polysaccharide lyase]]

1nkg

From Proteopedia

Current revision

Rhamnogalacturonan lyase from Aspergillus aculeatus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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