PDBsum entry 2avs

Hydrolase

PDB id: 2avs

Contents

Protein chains

99 a.a. *

Ligands

PO4 ×2

SO4

DMS

MK1

ACY ×4

Waters ×318

* Residue conservation analysis

PDB id:

2avs

Name:

Hydrolase

Title:

Kinetics, stability, and structural changes in high resolution crystal structures of HIV-1 protease with drug resistant mutations l24i, i50v, and g73s

Structure:

Pol polyprotein. Chain: a, b. Fragment: retropepsin. Synonym: HIV-1 protease. Engineered: yes. Other_details: complexed with indinavir

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.10Å R-factor: 0.109 R-free: 0.186

Authors:

F.Liu,P.I.Boross,Y.F.Wang,J.Tozser,J.M.Louis,R.W.Harrison,I.T.Weber

Key ref:

F.Liu et al. (2005). Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S. J Mol Biol, 354, 789-800. PubMed id: 16277992 DOI: 10.1016/j.jmb.2005.09.095

Date:

30-Aug-05 Release date: 24-Jan-06

Protein chains

P04587  (POL_HV1B5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH5)

Seq: 1447 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2005.09.095

J Mol Biol 354:789-800 (2005)

PubMed id: 16277992

Kinetic, stability, and structural changes in high-resolution crystal structures of HIV-1 protease with drug-resistant mutations L24I, I50V, and G73S.

F.Liu, P.I.Boross, Y.F.Wang, J.Tozser, J.M.Louis, R.W.Harrison, I.T.Weber.

ABSTRACT

The crystal structures, dimer stabilities, and kinetics have been analyzed for wild-type human immunodeficiency virus type 1 (HIV-1) protease (PR) and resistant mutants PR(L24I), PR(I50V), and PR(G73S) to gain insight into the molecular basis of drug resistance. The mutations lie in different structural regions. Mutation I50V alters a residue in the flexible flap that interacts with the inhibitor, L24I alters a residue adjacent to the catalytic Asp25, and G73S lies at the protein surface far from the inhibitor-binding site. PR(L24I) and PR(I50V), showed a 4% and 18% lower k(cat)/K(m), respectively, relative to PR. The relative k(cat)/K(m) of PR(G73S) varied from 14% to 400% when assayed using different substrates. Inhibition constants (K(i)) of the antiviral drug indinavir for the reaction catalyzed by the mutant enzymes were about threefold and 50-fold higher for PR(L24I) and PR(I50V), respectively, relative to PR and PR(G73S). The dimer dissociation constant (K(d)) was estimated to be approximately 20 nM for both PR(L24I) and PR(I50V), and below 5 nM for PR(G73S) and PR. Crystal structures of the mutants PR(L24I), PR(I50V) and PR(G73S) were determined in complexes with indinavir, or the p2/NC substrate analog at resolutions of 1.10-1.50 Angstrom. Each mutant revealed distinct structural changes relative to PR. The mutated residues in PR(L24I) and PR(I50V) had reduced intersubunit contacts, consistent with the increased K(d) for dimer dissociation. Relative to PR, PR(I50V) had fewer interactions of Val50 with inhibitors, in agreement with the dramatically increased K(i). The distal mutation G73S introduced new hydrogen bond interactions that can transmit changes to the substrate-binding site and alter catalytic activity. Therefore, the structural alterations observed for drug-resistant mutations were in agreement with kinetic and stability changes.

Selected figure(s)

Figure 1.
Figure 1. PR dimer structure (green ribbons) with indinavir (red bonds). The sites of mutation are indicated by black spheres for Leu24, Ile50 and Gly73. Only one subunit is labeled.

Figure 6.
Figure 6. Protease-inhibitor interactions. Only the residues involved in hydrogen bond interactions are shown. Water molecules are represented as spheres. Hydrogen bonds are indicated by broken lines. (a) PR[L24I] hydrogen bond interactions with indinavir. Water molecules are labeled A-D. (b) Interactions of Arg8' with the pyridyl group of indinavir in PR[I50V]-IDV. The omit map is contoured at 3.5s. (c) PR[L24I] interactions with p2/NC. Water molecules are labeled 1-8. Arg8 and Arg8' are omitted for clarity. (d) Selected interactions of the side-chains of Ile/Leu50 and 50' with indinavir in the PR[I50V] and PR indinavir complexes. PR-IDV is in green and PR[I50V]-IDV is red. Only the central portion of indinavir is shown with van der Waals contacts indicated by dotted lines with distances in Å.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2005, 354, 789-800) copyright 2005.

Figures were selected by an automated process.