7BZ0

complex structure of alginate lyase AlyF-OU02 with G6

Summary for 7BZ0

• Entry DOI: 10.2210/pdb7bz0/pdb
• Descriptor: Alginate lyase AlyF-OU02, alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: pl6, ca2+-independent, complex, substrate-binding mechanism., lyase
• Biological source: Vibrio splendidus
• Total number of polymer chains: 1
• Total formula weight: 60137.52

Authors

Liu, W.,Lyu, Q.,Zhang, K. (deposition date: 2020-04-26, release date: 2021-03-10, Last modification date: 2023-11-29)

Primary citation

Zhang, K.,Liu, T.,Liu, W.,Lyu, Q.
Structural insights into the substrate-binding cleft of AlyF reveal the first long-chain alginate-binding mode.
Acta Crystallogr D Struct Biol, 77:336-346, 2021

PubMed Abstract: 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.

PubMed: 33645537
DOI: 10.1107/S205979832100005X

Experimental method

X-RAY DIFFRACTION (1.8 Å)