Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography.
HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp-25 and Asp-125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9-A resolution and X-ray crystallography at 1.4-A resolution. The resulting structural data show that the catalytic residue Asp-25 is protonated and that Asp-125 (the catalytic residue from the corresponding diad-related molecule) is deprotonated. The proton on Asp-25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine (Apns) group in KNI-272. The deprotonated Asp-125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.
Adachi
Motoyasu
M
Molecular Structural Biology Group, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan.
Ohhara
Takashi
T
Kurihara
Kazuo
K
Tamada
Taro
T
Honjo
Eijiro
E
Okazaki
Nobuo
N
Arai
Shigeki
S
Shoyama
Yoshinari
Y
Kimura
Kaname
K
Matsumura
Hiroyoshi
H
Sugiyama
Shigeru
S
Adachi
Hiroaki
H
Takano
Kazufumi
K
Mori
Yusuke
Y
Hidaka
Koushi
K
Kimura
Tooru
T
Hayashi
Yoshio
Y
Kiso
Yoshiaki
Y
Kuroki
Ryota
R
D055162:Biocatalysis; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism; D017320:HIV Protease Inhibitors / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D033363:Neutron Diffraction; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D017320:HIV Protease Inhibitors; D009842:Oligopeptides; D014867:Water; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1; C077822:kynostatin 272