|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='3njv' size='340' side='right'caption='[[3njv]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='3njv' size='340' side='right'caption='[[3njv]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3njv]] 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=3NJV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3NJV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3njv]] 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=3NJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NJV 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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</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]] 2.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1nkg|1nkg]], [[3njx|3njx]]</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=GTR:BETA-D-GALACTOPYRANURONIC+ACID'>GTR</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3njv OCA], [https://pdbe.org/3njv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3njv RCSB], [https://www.ebi.ac.uk/pdbsum/3njv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3njv ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pectin_lyase Pectin lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.10 4.2.2.10] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3njv OCA], [http://pdbe.org/3njv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3njv RCSB], [http://www.ebi.ac.uk/pdbsum/3njv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3njv ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 17: |
Line 15: |
| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/3njv_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/3njv_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aspac]] | + | [[Category: Aspergillus aculeatus]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pectin lyase]]
| + | [[Category: Borchert TV]] |
| - | [[Category: Borchert, T V]] | + | [[Category: Christensen LLH]] |
| - | [[Category: Christensen, L L.H]] | + | [[Category: Christensen U]] |
| - | [[Category: Christensen, U]] | + | [[Category: Jensen MH]] |
| - | [[Category: Jensen, M H]] | + | [[Category: Larsen S]] |
| - | [[Category: Larsen, S]] | + | [[Category: Lo Leggio L]] |
| - | [[Category: Leggio, L Lo]] | + | [[Category: Otten H]] |
| - | [[Category: Otten, H]] | + | |
| - | [[Category: Carbohydrate active enzyme]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pectin degradation]]
| + | |
| - | [[Category: Polysaccharide lyase family 4]]
| + | |
| Structural highlights
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
We present here the first experimental evidence for bound substrate in the active site of a rhamnogalacturonan lyase belonging to family 4 of polysaccharide lyases, Aspergillus aculeatus rhamnogalacturonan lyase (RGL4). RGL4 is involved in the degradation of rhamnogalacturonan-I, an important pectic plant cell wall polysaccharide. Based on the previously determined wild-type structure, enzyme variants RGL4_H210A and RGL4_K150A have been produced and characterized both kinetically and structurally, showing that His210 and Lys150 are key active-site residues. Crystals of the RGL4_K150A variant soaked with a rhamnogalacturonan digest gave a clear picture of substrate bound in the -3/+3 subsites. The crystallographic and kinetic studies on RGL4, and structural and sequence comparison to other enzymes in the same and other PL families, enable us to propose a detailed reaction mechanism for the beta-elimination on [-,2)-alpha-l-rhamno-(1,4)-alpha-d-galacturonic acid-(1,-]. The mechanism differs significantly from the one established for pectate lyases, in which most often calcium ions are engaged in catalysis.
Structural and Biochemical Studies Elucidate the Mechanism of Rhamnogalacturonan Lyase from Aspergillus aculeatus.,Jensen MH, Otten H, Christensen U, Borchert TV, Christensen LL, Larsen S, Leggio LL J Mol Biol. 2010 Sep 17. PMID:20851126[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
- ↑ 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
|
