6sec: Difference between revisions
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The | ==Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cBon complex with ONPG== | ||
<StructureSection load='6sec' size='340' side='right'caption='[[6sec]], [[Resolution|resolution]] 2.77Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6sec]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_sp._32cB Arthrobacter sp. 32cB]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SEC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.768Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=145:1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE'>145</scene>, <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6sec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sec OCA], [https://pdbe.org/6sec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sec RCSB], [https://www.ebi.ac.uk/pdbsum/6sec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sec ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A023UGN9_9MICC A0A023UGN9_9MICC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
ArthbetaDG is a dimeric, cold-adapted beta-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthbetaDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthbetaDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: ArthbetaDG_E441Q/LACs and ArthbetaDG/IPTG (ligand bound in shallow mode) and structures of complexes ArthbetaDG_E441Q/LACd, ArthbetaDG/ONPG (ligands bound in deep mode), and galactose ArthbetaDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 betaDGs, in ArthbetaDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation. | |||
Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase from Arthrobacter sp. 32cB.,Rutkiewicz M, Bujacz A, Wanarska M, Wierzbicka-Wos A, Cieslinski H Int J Mol Sci. 2019 Sep 3;20(17). pii: ijms20174301. doi: 10.3390/ijms20174301. PMID:31484304<ref>PMID:31484304</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6sec" style="background-color:#fffaf0;"></div> | ||
[[Category: Bujacz | |||
[[Category: | ==See Also== | ||
*[[Galactosidase 3D structures|Galactosidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arthrobacter sp. 32cB]] | |||
[[Category: Large Structures]] | |||
[[Category: Bujacz A]] | |||
[[Category: Bujacz G]] | |||
[[Category: Rutkiewicz M]] | |||
Latest revision as of 15:40, 24 January 2024
Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cBon complex with ONPGCold-adapted beta-D-galactosidase from Arthrobacter sp. 32cBon complex with ONPG
Structural highlights
FunctionPublication Abstract from PubMedArthbetaDG is a dimeric, cold-adapted beta-d-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthbetaDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthbetaDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The resulting three-dimensional structures of complexes: ArthbetaDG_E441Q/LACs and ArthbetaDG/IPTG (ligand bound in shallow mode) and structures of complexes ArthbetaDG_E441Q/LACd, ArthbetaDG/ONPG (ligands bound in deep mode), and galactose ArthbetaDG/GAL and their analysis enabled structural characterization of the hydrolysis reaction mechanism. Furthermore, comparative analysis with mesophilic analogs revealed the most striking differences in catalysis mechanisms. The key role in substrate transfer from shallow to deep binding mode involves rotation of the F581 side chain. It is worth noting that the 10-aa loop restricting access to the active site in mesophilic GH2 betaDGs, in ArthbetaDG is moved outward. This facilitates access of substrate to active site. Such a permanent exposure of the entrance to the active site may be a key factor for improved turnover rate of the cold adapted enzyme and thus a structural feature related to its cold adaptation. Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase from Arthrobacter sp. 32cB.,Rutkiewicz M, Bujacz A, Wanarska M, Wierzbicka-Wos A, Cieslinski H Int J Mol Sci. 2019 Sep 3;20(17). pii: ijms20174301. doi: 10.3390/ijms20174301. PMID:31484304[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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