3njv: Difference between revisions
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==Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex== | |||
=== | <StructureSection load='3njv' size='340' side='right' caption='[[3njv]], [[Resolution|resolution]] 2.40Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3njv]] 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=3NJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NJV 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>, <scene name='pdbligand=GTR:GALACTURONIC+ACID'>GTR</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></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='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 Aspergillus aculeatus])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3njv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3njv RCSB], [http://www.ebi.ac.uk/pdbsum/3njv 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/nj/3njv_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 == | |||
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<ref>PMID:20851126</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
== | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aspergillus aculeatus]] | [[Category: Aspergillus aculeatus]] | ||
[[Category: Pectin lyase]] | [[Category: Pectin lyase]] | ||
[[Category: Borchert, T V | [[Category: Borchert, T V]] | ||
[[Category: Christensen, L L.H | [[Category: Christensen, L L.H]] | ||
[[Category: Christensen, U | [[Category: Christensen, U]] | ||
[[Category: Jensen, M H | [[Category: Jensen, M H]] | ||
[[Category: Larsen, S | [[Category: Larsen, S]] | ||
[[Category: Leggio, L Lo | [[Category: Leggio, L Lo]] | ||
[[Category: Otten, H | [[Category: Otten, H]] | ||
[[Category: Carbohydrate active enzyme]] | [[Category: Carbohydrate active enzyme]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Pectin degradation]] | [[Category: Pectin degradation]] | ||
[[Category: Polysaccharide lyase family 4]] | [[Category: Polysaccharide lyase family 4]] | ||
