9L2Z

Zn-Carbonic Anhydrase II complexed with 3NPA at 120 K

9L2Z の概要

• エントリーDOI: 10.2210/pdb9l2z/pdb
• 関連するPDBエントリー: 7Y2A
• 分子名称: Carbonic anhydrase 2, ZINC ION, 2-(3-NITROPHENYL)ACETIC ACID, ... (4 entities in total)
• 機能のキーワード: carbonic anhydrase, enzyme mechanism, metalloenzymes, metal binding protein
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 29535.62

構造登録者

Kim, C.U.,Kim, J.K. (登録日: 2024-12-17, 公開日: 2025-04-30, 最終更新日: 2025-05-21)

主引用文献

Kim, J.K.,Lim, S.W.,Jeong, H.,Lee, C.,Kim, S.,Son, D.W.,Kumar, R.,Andring, J.T.,Lomelino, C.,Wierman, J.L.,Cohen, A.E.,Shin, T.J.,Ghim, C.M.,McKenna, R.,Jo, B.H.,Min, D.,Choi, J.M.,Kim, C.U.
Fast product release requires active-site water dynamics in carbonic anhydrase.
Nat Commun, 16:4404-4404, 2025

PubMed Abstract: Water plays an essential role in enzyme structure, stability, and the substantial rate enhancement of enzyme catalysis. However, direct observations linking enzyme catalysis and active-site water dynamics pose a significant challenge due to experimental difficulties. By integrating an ultraviolet (UV) photolysis technique with temperature-controlled X-ray crystallography, we track the catalytic pathway of carbonic anhydrase II (CAII) at 1.2 Å resolution. This approach enables us to construct molecular movies of CAII catalysis, encompassing substrate (CO) binding, conversion from substrate to product (bicarbonate), and product release. In the catalytic pathway, we identify an unexpected configuration in product binding and correlate it with sub-nanosecond rearrangement of active-site water. Based on these experimental observations, we propose a comprehensive mechanism of CAII and describe the detailed structure and dynamics of active-site water in CAII. Our findings suggest that CAII has evolved to utilize the structure and fast dynamics of the active-site waters for its diffusion-limited catalytic efficiency.

PubMed: 40355440
DOI: 10.1038/s41467-025-59645-x

実験手法

X-RAY DIFFRACTION (1.2 Å)