4GPG

X/N joint refinement of Achromobacter Lyticus Protease I free form at pD8.0

4GPG の概要

• エントリーDOI: 10.2210/pdb4gpg/pdb
• 分子名称: Protease 1 (2 entities in total)
• 機能のキーワード: lysine specific serine protease, hydrolase
• 由来する生物種: Achromobacter lyticus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 27759.23

構造登録者

Ohnishi, Y.,Yamada, T.,Kurihara, K.,Tanaka, I.,Sakiyama, F.,Masaki, T.,Niimura, N. (登録日: 2012-08-21, 公開日: 2013-09-11, 最終更新日: 2024-10-30)

主引用文献

Ohnishi, Y.,Yamada, T.,Kurihara, K.,Tanaka, I.,Sakiyama, F.,Masaki, T.,Niimura, N.
Neutron and X-ray crystallographic analysis of Achromobacter protease I at pD 8.0: protonation states and hydration structure in the free-form.
Biochim.Biophys.Acta, 1834:1642-1647, 2013

PubMed Abstract: The structure of the free-form of Achromobacter protease I (API) at pD 8.0 was refined by simultaneous use of single crystal X-ray and neutron diffraction data sets to investigate the protonation states of key catalytic residues of the serine protease. Occupancy refinement of the catalytic triad in the active site of API free-form showed that ca. 30% of the imidazole ring of H57 and ca. 70% of the hydroxyl group of S194 were deuterated. This observation indicates that a major fraction of S194 is protonated in the absence of a substrate. The protonation state of the catalytic triad in API was compared with the bovine β-trypsin-BPTI complex. The comparison led to the hypothesis that close contact of a substrate with S194 could lower the acidity of its hydroxyl group, thereby allowing H57 to extract the hydrogen from the hydroxyl group of S194. H210, which is a residue specific to API, does not form a hydrogen bond with the catalytic triad residue D113. Instead, H210 forms a hydrogen bond network with S176, H177 and a water molecule. The close proximity of the bulky, hydrophobic residue W169 may protect this hydrogen bond network, and this protection may stabilize the function of API over a wide pH range.

PubMed: 23714114
DOI: 10.1016/j.bbapap.2013.05.012

実験手法

NEUTRON DIFFRACTION (1.979 Å)
X-RAY DIFFRACTION (1.895 Å)