5YRS

X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Its SIHB with Catalytic Aspartate

Replaces:  3MIM

Summary for 5YRS

• Entry DOI: 10.2210/pdb5yrs/pdb
• Related: 1G6L 1LV1 2NPH
• Descriptor: PROTEASE, RT-RH oligopeprtide, ... (4 entities in total)
• Functional Keywords: hiv-1 protease, tetrahedral intermediate, short ionic hydrogen bond, substrate complex, rt-rh, hydrolase
• Biological source: Human immunodeficiency virus 1 (HIV-1); More
• Cellular location: Gag-Pol polyprotein: Host cell membrane; Lipid-anchor . Matrix protein p17: Virion membrane; Lipid- anchor . Capsid protein p24: Virion . Nucleocapsid protein p7: Virion . Reverse transcriptase/ribonuclease H: Virion . Integrase: Virion : P04585 P04585
• Total number of polymer chains: 3
• Total formula weight: 23040.88

Authors

Das, A.,Mahale, S.,Prashar, V.,Bihani, S.,Ferrer, J.-L.,Hosur, M.V. (deposition date: 2017-11-10, release date: 2018-03-07, Last modification date: 2024-11-13)

Primary citation

Das, A.,Mahale, S.,Prashar, V.,Bihani, S.,Ferrer, J.L.,Hosur, M.V.
X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate.
J. Am. Chem. Soc., 132:6366-6373, 2010

PubMed Abstract: Structural snapshots of each step in the catalytic cycle would help development of inhibitors of human immunodeficiency virus type 1 protease (HIV-1 PR) as effective drugs against HIV/AIDS. We report here one snapshot obtained by determining the structure of enzyme-substrate complex under conditions where the catalytic activity of the enzyme is greatly reduced. The 1.76 A crystal structure shows the oligopeptide substrate, AETFYVDGAA, converted in situ into a gem-diol tetrahedral intermediate (TI). The gem-diol intermediate is neutral and one of the hydroxyl oxygens forms a very short hydrogen bond (2.2 A) with the anionic aspartate of the catalytic dyad, which is monoprotonated. Further, there is no hydrogen atom on the outer oxygen of the neutral aspartate. These two observations provide direct evidence that, in the reaction mechanism, hydrogen bonding between catalytic aspartate and scissile carbonyl oxygen facilitates water attack on the scissile carbon atom. Comparison with the structural snapshot of the biproduct complex involving the same substrate reveals the reorganization of the hydrogen bonds at the catalytic center as the enzymatic reaction progresses toward completion. Accumulation of TI in the crystals provides direct evidence that collapse of TI is the rate-limiting step of hydrolysis.

PubMed: 20397633
DOI: 10.1021/ja100002b

Experimental method

X-RAY DIFFRACTION (1.76 Å)