6ik7: Difference between revisions
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==Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose== | ==Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose== | ||
<StructureSection load='6ik7' size='340' side='right' caption='[[6ik7]], [[Resolution|resolution]] 3.10Å' scene=''> | <StructureSection load='6ik7' size='340' side='right'caption='[[6ik7]], [[Resolution|resolution]] 3.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6ik7]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6ik7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IK7 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</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=6ik7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ik7 OCA], [https://pdbe.org/6ik7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ik7 RCSB], [https://www.ebi.ac.uk/pdbsum/6ik7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ik7 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/O81100_SOLLC O81100_SOLLC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
MAIN CONCLUSION: TBG4 recognize multiple linkage types substrates due to having a spatially wide subsite + 1. This feature allows the degradation of AGI, AGII, and AGP leading to the fruit ripening. beta-galactosidase (EC 3. 2. 1. 23) catalyzes the hydrolysis of beta-galactan and release of D-galactose. Tomato has at least 17 beta-galactosidases (TBGs), of which, TBG 4 is responsible for fruit ripening. TBG4 hydrolyzes not only beta-1,4-bound galactans, but also beta-1,3- and beta-1,6-galactans. In this study, we compared each enzyme-substrate complex using X-ray crystallography, ensemble refinement, and docking simulation to understand the broad substrate-specificity of TBG4. In subsite - 1, most interactions were conserved across each linkage type of galactobioses; however, some differences were seen in subsite + 1, owing to the huge volume of catalytic pocket. In addition to this, docking simulation indicated TBG4 to possibly have more positive subsites to recognize and hydrolyze longer galactans. Taken together, our results indicated that during tomato fruit ripening, TBG4 plays an important role by degrading arabinogalactan I (AGI), arabinogalactan II (AGII), and the carbohydrate moiety of arabinogalactan protein (AGP). | |||
Substrate-recognition mechanism of tomato beta-galactosidase 4 using X-ray crystallography and docking simulation.,Matsuyama K, Kondo T, Igarashi K, Sakamoto T, Ishimaru M Planta. 2020 Oct 3;252(4):72. doi: 10.1007/s00425-020-03481-4. PMID:33011862<ref>PMID:33011862</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6ik7" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Solanum lycopersicum]] | ||
[[Category: Igarashi | [[Category: Igarashi K]] | ||
[[Category: Ishimaru | [[Category: Ishimaru M]] | ||
[[Category: Matsuyama | [[Category: Matsuyama K]] | ||
[[Category: Nakae | [[Category: Nakae S]] | ||
[[Category: Tada | [[Category: Tada T]] | ||
Latest revision as of 09:44, 22 November 2023
Crystal structure of tomato beta-galactosidase (TBG) 4 in complex with beta-1,3-galactobiose
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