This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
7bz0
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 7bz0 is ON HOLD Authors: Liu, W.Z., Lyu, Q.Q., Zhang, K.K. Description: complex structure of alginate lyase AlyF-OU02 with G6 [[Category: Unrelease...) |
|||
| (3 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | '''Unreleased structure''' | ||
| - | + | ==complex structure of alginate lyase AlyF-OU02 with G6== | |
| + | <StructureSection load='7bz0' size='340' side='right'caption='[[7bz0]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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='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> | ||
| + | == 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> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 7bz0" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Vibrio splendidus]] | ||
| + | [[Category: Liu W]] | ||
| + | [[Category: Lyu Q]] | ||
| + | [[Category: Zhang K]] | ||
Current revision
complex structure of alginate lyase AlyF-OU02 with G6
| |||||||||||
