PDBsum entry 1k2b

Hydrolase/hydrolase inhibitor

PDB id: 1k2b

Contents

Protein chains

99 a.a. *

Ligands

0Q4

Waters ×128

* Residue conservation analysis

PDB id:

1k2b

Name:

Hydrolase/hydrolase inhibitor

Title:

Combining mutations in HIV-1 protease to understand mechanisms of resistance

Structure:

Protease retropepsin. Chain: a, b. Synonym: retropepsin, pr. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Trimer (from PQS)

Resolution:

1.70Å R-factor: 0.215 R-free: 0.278

Authors:

B.Mahalingam,P.Boross,Y.-F.Wang,J.M.Louis,C.Fischer,J.Tozser,R.W Harrison,I.T.Weber

Key ref:

B.Mahalingam et al. (2002). Combining mutations in HIV-1 protease to understand mechanisms of resistance. Proteins, 48, 107-116. PubMed id: 12012342 DOI: 10.1002/prot.10140

Date:

26-Sep-01 Release date: 10-Jul-02

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 7 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
• 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: 10.1002/prot.10140

Proteins 48:107-116 (2002)

PubMed id: 12012342

Combining mutations in HIV-1 protease to understand mechanisms of resistance.

B.Mahalingam, P.Boross, Y.F.Wang, J.M.Louis, C.C.Fischer, J.Tozser, R.W.Harrison, I.T.Weber.

ABSTRACT

HIV-1 develops resistance to protease inhibitors predominantly by selecting mutations in the protease gene. Studies of resistant mutants of HIV-1 protease with single amino acid substitutions have shown a range of independent effects on specificity, inhibition, and stability. Four double mutants, K45I/L90M, K45I/V82S, D30N/V82S, and N88D/L90M were selected for analysis on the basis of observations of increased or decreased stability or enzymatic activity for the respective single mutants. The double mutants were assayed for catalysis, inhibition, and stability. Crystal structures were analyzed for the double mutants at resolutions of 2.2-1.2 A to determine the associated molecular changes. Sequence-dependent changes in protease-inhibitor interactions were observed in the crystal structures. Mutations D30N, K45I, and V82S showed altered interactions with inhibitor residues at P2/P2', P3/P3'/P4/P4', and P1/P1', respectively. One of the conformations of Met90 in K45I/L90M has an unfavorably close contact with the carbonyl oxygen of Asp25, as observed previously in the L90M single mutant. The observed catalytic efficiency and inhibition for the double mutants depended on the specific substrate or inhibitor. In particular, large variation in cleavage of p6(pol)-PR substrate was observed, which is likely to result in defects in the maturation of the protease from the Gag-Pol precursor and hence viral replication. Three of the double mutants showed values for stability that were intermediate between the values observed for the respective single mutants. D30N/V82S mutant showed lower stability than either of the two individual mutations, which is possibly due to concerted changes in the central P2-P2' and S2-S2' sites. The complex effects of combining mutations are discussed.

Selected figure(s)

Figure 1.
Figure 1. Location of the mutations in HIV-1 protease dimer. Residues 1-99 correspond to one monomer of the homodimer. The sites of mutations are indicated by ball-and-stick representations. The residue numbers of the mutations are labeled in one subunit.

Figure 3.
Figure 3. Electron density map contoured at 1.8 level for the catalytic aspartates in the K45I/V82S crystal structure refined at 1.2 Å.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2002, 48, 107-116) copyright 2002.

Figures were selected by an automated process.