7bz0
From Proteopedia
(Difference between revisions)
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==complex structure of alginate lyase AlyF-OU02 with G6== | ==complex structure of alginate lyase AlyF-OU02 with G6== | ||
| - | <StructureSection load='7bz0' size='340' side='right'caption='[[7bz0]]' scene=''> | + | <StructureSection load='7bz0' size='340' side='right'caption='[[7bz0]], [[Resolution|resolution]] 1.80Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7bz0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_splendidus Vibrio splendidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BZ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BZ0 FirstGlance]. <br> |
| - | </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=7bz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz0 OCA], [https://pdbe.org/7bz0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz0 ProSAT]</span></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]] 1.8Å</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=LGU:ALPHA-L-GULURONATE'>LGU</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=7bz0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bz0 OCA], [https://pdbe.org/7bz0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bz0 RCSB], [https://www.ebi.ac.uk/pdbsum/7bz0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bz0 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A0A2S7V3I3_VIBSP A0A2S7V3I3_VIBSP] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The products of alginate degradation, alginate oligosaccharides (AOS), have potential applications in many areas, including functional foods and marine drugs. Enzyme-based approaches using alginate lyases have advantages in the preparation of well defined AOS and have attracted much attention in recent years. However, a lack of structural insight into the whole substrate-binding cleft for most known alginate lyases severely hampers their application in the industrial generation of well defined AOS. To solve this issue, AlyF was co-crystallized with the long alginate oligosaccharide G6 (L-hexaguluronic acid hexasodium salt), which is the longest bound substrate in all solved alginate lyase complex structures. AlyF formed interactions with G6 from subsites -3 to +3 without additional substrate-binding site interactions, suggesting that the substrate-binding cleft of AlyF was fully occupied by six sugars, which was further confirmed by isothermal titration calorimetry and differential scanning calorimetry analyses. More importantly, a combination of structural comparisons and mutagenetic analyses determined that three key loops (loop 1, Lys215-Glu236; loop 2, Gln402-Ile416; loop 3, Arg334-Gly348) mainly function in binding long substrates (degree of polymerization of >4). The potential flexibility of loop 1 and loop 2 might enable the substrate to continue to enter the cleft after binding to subsites +1 to +3; loop 3 stabilizes and orients the substrate at subsites -2 and -3. Taken together, these results provide the first possible alginate lyase-substrate binding profile for long-chain alginates, facilitating the rational design of new enzymes for industrial purposes. | ||
| + | |||
| + | Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode.,Zhang K, Liu T, Liu W, Lyu Q Acta Crystallogr D Struct Biol. 2021 Mar 1;77(Pt 3):336-346. doi:, 10.1107/S205979832100005X. Epub 2021 Feb 17. PMID:33645537<ref>PMID:33645537</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7bz0" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Vibrio splendidus]] | ||
[[Category: Liu W]] | [[Category: Liu W]] | ||
[[Category: Lyu Q]] | [[Category: Lyu Q]] | ||
[[Category: Zhang K]] | [[Category: Zhang K]] | ||
Current revision
complex structure of alginate lyase AlyF-OU02 with G6
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