7KV0

Crystallographic structure of Paenibacillus xylanivorans GH11

7KV0 の概要

• エントリーDOI: 10.2210/pdb7kv0/pdb
• 分子名称: Endo-1,4-beta-xylanase, 1,2-ETHANEDIOL (3 entities in total)
• 機能のキーワード: glycoside hydrolase, gh11, hydrolase
• 由来する生物種: Paenibacillus sp. A59
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 40864.04

構造登録者

Briganti, L.,Polikarpov, I. (登録日: 2020-11-26, 公開日: 2021-09-29, 最終更新日: 2023-10-18)

主引用文献

Briganti, L.,Capetti, C.,Pellegrini, V.O.A.,Ghio, S.,Campos, E.,Nascimento, A.S.,Polikarpov, I.
Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase.
Comput Struct Biotechnol J, 19:1557-1566, 2021

PubMed Abstract: Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from (Xyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The Xyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of Xyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.

PubMed: 33815691
DOI: 10.1016/j.csbj.2021.03.002

実験手法

X-RAY DIFFRACTION (2.501 Å)