Primary Citation PubMed: 12051725
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Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis.
(2009) PLoS One 4
PubMed: 19924250 | PubMedCentral: PMC2775671 | DOI: 10.1371/journal.pone.0007860
Figure 4 also shows the position of the catalytic water observed in the structure of unliganded HIV-1 protease (PDB Id 1LV1).
WAT1 is shifted by about 1.4 Å from the corresponding water molecule coordinating both catalytic aspartates in the unliganded structures (PDB Id 1LV1 and 2G69).
Each figure is based on the structure indicated: (a) catalytic water molecule bound symmetrically to the two aspartates (structure PDB Id 1LV1), (b) movement of catalytic water to position WAT1 with binding of substrate (modelled), (c) attack by WAT1 and formation of tetrahedral intermediate (Structure TI), (d) cleavage of the peptide bond with product peptides still bound in the active site (structure PDB Id 2NPH), (e) diffusion of P product out of and WAT1 into active site (present structure), and (f) release of Q product and movement of WAT1 into original position (PDB Id 1LV1).
g004 Figure 4 Relative positions of WAT1 and the modelled substrate in the active site: Diagram showing superposition of three structures: 1) present structure (yellow carbon), 2) unliganded HIV-1 protease (magenta carbon, PDB Id 1LV1) and 3) inactive HIV-1 protease/substrate complex (green carbon, PDB Id 1KJH).
A water molecule found symmetrically hydrogen bonded to carboxyl oxygen atoms of both catalytic aspartates in the high resolution crystal structures of unliganded enzyme, (PDB Id 1LV1 and 2G69) is believed to be the nucleophile.
Computer program Phaser  –  from CCP4 suite was used to obtain molecular replacement solution using the structure 1LV1  ,  as the search model.
Publication Year: 2009
Mining the protein data bank to differentiate error from structural variation in clustered static structures: an examination of HIV protease.
(2012) Viruses 4
PubMed: 22590675 | PubMedCentral: PMC3347031 | DOI: 10.3390/v4030348
Several exhibited the closed flap conformation, though closer examination revealed these to belong to covalently-bonded PR dimers (PDB IDs 1g6l and 1lv1) that were split into monomers by removing the ... ridge of connecting residues.
Publication Year: 2012
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