2VS2

Neutron diffraction structure of endothiapepsin in complex with a gem- diol inhibitor.

2VS2 の概要

• エントリーDOI: 10.2210/pdb2vs2/pdb
• 関連するPDBエントリー: 1E5O 1E80 1E81 1E82 1EED 1ENT 1EPL 1EPM 1EPN 1EPO 1EPP 1EPQ 1EPR 1ER8 1GKT 1GVT 1GVU 1GVV 1GVW 1GVX 1OD1 1OEW 1OEX 2ER0 2ER6 2ER7 2ER9 2JJI 2JJJ 2V00 3ER3 3ER5 4APE 4ER1 4ER2 4ER4 5ER1 5ER2
• 関連するBIRD辞書のPRD_ID: PRD_000361
• 分子名称: ENDOTHIAPEPSIN, N~2~-[(2R)-2-benzyl-3-(tert-butylsulfonyl)propanoyl]-N-{(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-[(2-morpholin-4-ylethyl)amino]-4-oxobutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide (3 entities in total)
• 機能のキーワード: acid proteinase, aspartyl protease, zymogen, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• 由来する生物種: CRYPHONECTRIA PARASITICA (CHESTNUT BLIGHT FUNGUS)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34580.77

構造登録者

Coates, L.,Tuan, H.-F.,Tomanicek, S.,Kovalevsky, A.,Mustyakimov, M.,Erskine, P.,Cooper, J. (登録日: 2008-04-17, 公開日: 2008-05-27, 最終更新日: 2023-11-15)

主引用文献

Coates, L.,Tuan, H.-F.,Tomanicek, S.,Kovalevsky, A.,Mustyakimov, M.,Erskine, P.,Cooper, J.
The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-Ray Diffraction
J.Am.Chem.Soc., 130:7235-, 2008

PubMed Abstract: Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.

PubMed: 18479128
DOI: 10.1021/JA801269X

実験手法

NEUTRON DIFFRACTION (2 Å)