6f2p: Difference between revisions
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<StructureSection load='6f2p' size='340' side='right' caption='[[6f2p]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='6f2p' size='340' side='right' caption='[[6f2p]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6f2p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F2P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F2P FirstGlance]. <br> | <table><tr><td colspan='2'>[[6f2p]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_polymyxa_group Bacillus polymyxa group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F2P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6F2P FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xanthan_lyase Xanthan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.12 4.2.2.12] </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=6f2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f2p OCA], [http://pdbe.org/6f2p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f2p RCSB], [http://www.ebi.ac.uk/pdbsum/6f2p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f2p 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=6f2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f2p OCA], [http://pdbe.org/6f2p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6f2p RCSB], [http://www.ebi.ac.uk/pdbsum/6f2p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6f2p ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
We have characterized the structure and dynamics of the carbohydrate-modifying enzyme Paenibacillus nanensis xanthan lyase (PXL) involved in the degradation of xanthan by X-ray crystallography, small-angle X-ray scattering, and hydrogen/deuterium exchange mass spectrometry. Unlike other xanthan lyases, PXL is specific for both unmodified mannose and pyruvylated mannose, which we find is correlated with structural differences in the substrate binding groove. The structure of the full-length enzyme reveals two additional C-terminal modules, one of which belongs to a new non-catalytic carbohydrate binding module family. Ca(2+) are critical for the activity and conformation of PXL, and we show that their removal by chelating agents results in localized destabilization/unfolding of particularly the C-terminal modules. We use the structure and the revealed impact of Ca(2+) coordination on conformational dynamics to guide the engineering of PXL variants with increased activity and stability in a chelating environment, thus expanding the possibilities for industrial applications of PXL. | |||
Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity.,Jensen PF, Kadziola A, Comamala G, Segura DR, Anderson L, Poulsen JN, Rasmussen KK, Agarwal S, Sainathan RK, Monrad RN, Svendsen A, Nielsen JE, Lo Leggio L, Rand KD Cell Chem Biol. 2018 Nov 9. pii: S2451-9456(18)30376-3. doi:, 10.1016/j.chembiol.2018.10.016. PMID:30503284<ref>PMID:30503284</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6f2p" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus polymyxa group]] | |||
[[Category: Xanthan lyase]] | [[Category: Xanthan lyase]] | ||
[[Category: Kadziola, A]] | [[Category: Kadziola, A]] | ||