PDBsum entry 3dox

Hydrolase

PDB id: 3dox

Contents

Protein chain

198 a.a.

Ligands

SER-GLN-ASN-TYR

PRO-ILE-VAL

Waters ×193

References listed in PDB file

Key reference

Title

X-Ray structure of HIV-1 protease in situ product complex.

Authors

S.Bihani, A.Das, V.Prashar, J.L.Ferrer, M.V.Hosur.

Ref.

Proteins, 2008, 74, 594-602. [DOI no: 10.1002/prot.22174]

PubMed id

18704947

Abstract

HIV-1 protease is an effective target for design of different types of drugs against AIDS. HIV-1 protease is also one of the few enzymes that can cleave substrates containing both proline and nonproline residues at the cleavage site. We report here the first structure of HIV-1 protease complexed with the product peptides SQNY and PIV derived by in situ cleavage of the oligopeptide substrate SQNYPIV, within the crystals. In the structure, refined against 2.0-A resolution synchrotron data, a carboxyl oxygen of SQNY is hydrogen-bonded with the N-terminal nitrogen atom of PIV. At the same time, this proline nitrogen atom does not form any hydrogen bond with catalytic aspartates. These two observations suggest that the protonation of scissile nitrogen, during peptide bond cleavage, is by a gem-hydroxyl of the tetrahedral intermediate rather than by a catalytic aspartic acid. Proteins 2009. (c) 2008 Wiley-Liss, Inc.

Figure 2.
Figure 2. Stereodiagram superposing present structure (yellow carbon) with the structure of hydroxy-inhibitor (JG365) complex(green) [PDB ID 2J9J]. The putative catalytic water H4 (orange sphere) is at 1.4 Å from the hydroxyl oxygen of the inhibitor. The flap water molecules (FW) for the two structures are also drawn.

Figure 3.
Figure 3. Hydrogen bonding interactions: (A) in the active site cavity. Full occupancy water molecules are shown as green spheres. Partial occupancy water molecules are shown as red spheres. Hydrogen bonds between partial water molecules are drawn in purple. (B) involving P1, P1 , H4, and catalytic aspartate residues. Interatomic distances are given in Å units.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 74, 594-602) copyright 2008.

Secondary reference #1

Title

1.9 a X-Ray study shows closed flap conformation in crystals of tethered HIV-1 pr.

Authors

B.Pillai, K.K.Kannan, M.V.Hosur.

Ref.

Proteins, 2001, 43, 57-64. [DOI no: 10.1002/1097-0134(20010401)43:1<57::AID-PROT1017>3.0.CO;2-D]

PubMed id

11170214

Figure 3.
Figure 3. Hydrogen bonding networks involving water molecules W1-W9 (red spheres) located in the active site, linking the flaps to the core of the enzyme. W1 is within hydrogen bonding distances from carboxyl groups of both catalytic aspartic acids: D25 and D1025. Such a water molecule is found in all native structures of HIV PR and is implicated in nucleophilic attack on the scissile peptide bond.

Figure 6.
Figure 6. Stereo view of the F[o]-F[c] electron-density map around Cys1095. Extra electron density clearly seen in the maps contoured at the 3 level. Similar density also observed around the sulfur atom of Cys67 and Cys1067.

The above figures are reproduced from the cited reference with permission from John Wiley & Sons, Inc.

Secondary reference #2

Title

Observation of a tetrahedral reaction intermediate in the HIV-1 protease-Substrate complex.

Authors

M.Kumar, V.Prashar, S.Mahale, M.V.Hosur.

Ref.

Biochem J, 2005, 389, 365-371.

PubMed id

15794743

Secondary reference #3

Title

Rapid screening for HIV-1 protease inhibitor leads through X-Ray diffraction.

Authors

B.Pillai, K.K.Kannan, S.V.Bhat, M.V.Hosur.

Ref.

Acta Crystallogr D Biol Crystallogr, 2004, 60, 594-596. [DOI no: 10.1107/S0907444903029676]

PubMed id

14993705

Figure 2.
Figure 2 Hydrogen-bonding interactions of acetyl-pepstatin (green) in orientation A bound in the active-site cavity of HIV-1 PR (yellow).

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #4

Title

Crystal structure of HIV-1 protease in situ product complex and observation of a low-Barrier hydrogen bond between catalytic aspartates.

Authors

A.Das, V.Prashar, S.Mahale, L.Serre, J.L.Ferrer, M.V.Hosur.

Ref.

Proc Natl Acad Sci U S A, 2006, 103, 18464-18469. [DOI no: 10.1073/pnas.0605809103]

PubMed id

17116869

Figure 2.
Fig. 2. Stereo diagrams of electron density maps. (A) 2F[o] – F[c] map in blue and F[o] – F[c] map in red when the substrate model refined is of a regular peptide. The peptide bond is in the negative density of the F[o] – F[c] map. (B) 2F[o] – F[c] omit map overlaid with the three models: regular peptide model (cyan), tetrahedral hydrated peptide model (brown), and cleaved peptide model (atomic color). Omit density for P1, P3, P1', and P3' residues defines the single orientation of the substrate.

Figure 3.
Fig. 3. Hydrogen-bonding interactions at the catalytic center are shown by dotted lines.