PDBsum entry 1fff

Hydrolase/hydrolase inhibitor

PDB id: 1fff

Contents

Protein chains

99 a.a. *

Ligands

0Q4

Waters ×105

* Residue conservation analysis

PDB id:

1fff

Name:

Hydrolase/hydrolase inhibitor

Title:

Structural implications of drug resistant mutants of HIV-1 protease : high resolution crystal structures of the mutant protease/substrate analog complexes.

Structure:

Protease retropepsin. Chain: c, d. 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:

1.90Å R-factor: 0.212 R-free: 0.248

Authors:

B.Mahalingam,J.M.Louis,R.W.Harrison,I.T.Weber

Key ref:

B.Mahalingam et al. (2001). Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes. Proteins, 43, 455-464. PubMed id: 11340661 DOI: 10.1002/prot.1057

Date:

25-Jul-00 Release date: 01-Jun-01

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
• 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.1057

Proteins 43:455-464 (2001)

PubMed id: 11340661

Structural implications of drug-resistant mutants of HIV-1 protease: high-resolution crystal structures of the mutant protease/substrate analogue complexes.

B.Mahalingam, J.M.Louis, J.Hung, R.W.Harrison, I.T.Weber.

ABSTRACT

Emergence of drug-resistant mutants of HIV-1 protease is an ongoing problem in the fight against AIDS. The mechanisms governing resistance are both complex and varied. We have determined crystal structures of HIV-1 protease mutants, D30N, K45I, N88D, and L90M complexed with peptide inhibitor analogues of CA-p2 and p2-NC cleavage sites in the Gag-pol precursor in order to study the structural mechanisms underlying resistance. The structures were determined at 1.55-1.9-A resolution and compared with the wild-type structure. The conformational disorder seen for most of the hydrophobic side-chains around the inhibitor binding site indicates flexibility of binding. Eight water molecules are conserved in all 9 structures; their location suggests that they are important for catalysis as well as structural stability. Structural differences among the mutants were analyzed in relation to the observed changes in protease activity and stability. Mutant L90M shows steric contacts with the catalytic Asp25 that could destabilize the catalytic loop at the dimer interface, leading to its observed decreased dimer stability and activity. Mutant K45I reduces the mobility of the flap and the inhibitor and contributes to an enhancement in structural stability and activity. The side-chain variations at residue 30 relative to wild-type are the largest in D30N and the changes are consistent with the altered activity observed with peptide substrates. Polar interactions in D30N are maintained, in agreement with the observed urea sensitivity. The side-chains of D30N and N88D are linked through a water molecule suggesting correlated changes at the two sites, as seen with clinical inhibitors. Structural changes seen in N88D are small; however, water molecules that mediate interactions between Asn88 and Thr74/Thr31/Asp30 in other complexes are missing in N88D.

Selected figure(s)

Figure 2.
Figure 2. Hydrophobic residues around the inhibitor with poorly defined electron density for the side-chains are shown in black. The catalytic aspartates are shown in gray.

Figure 3.
Figure 3. Superposition of inhibitors. The CA-p2 inhibitors are in black and the p2-NC inhibitors are in gray. All mutants were superposed onto the wild-type/p2-NC complex.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2001, 43, 455-464) copyright 2001.

Figures were selected by an automated process.