PDBsum entry 2whh

Hydrolase

PDB id: 2whh

Contents

Protein chain

198 a.a. *

Ligands

PPN-GLU ×2

Waters ×187

* Residue conservation analysis

PDB id:

2whh

Name:

Hydrolase

Title:

HIV-1 protease tethered dimer q-product complex along with nucleophilic water molecule

Structure:

Pol protein. Chain: a. Fragment: residues 7-105. Synonym: HIV-1 protease. Engineered: yes. Mutation: yes. Other_details: 5 residue peptide link between c terminus of first sub-unit and the n terminus of the second sub-unit of the dimer to produce a tethered dimer of HIV-1 protease (also see remark 999)

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.69Å R-factor: 0.219 R-free: 0.256

Authors:

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

Key ref:

V.Prashar et al. (2009). Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis. Plos One, 4, e7860. PubMed id: 19924250

Date:

05-May-09 Release date: 01-Dec-09

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 198 a.a.*

* PDB and UniProt seqs differ at 93 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

Plos One 4:e7860 (2009)

PubMed id: 19924250

Catalytic water co-existing with a product peptide in the active site of HIV-1 protease revealed by X-ray structure analysis.

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

ABSTRACT

BACKGROUND: It is known that HIV-1 protease is an important target for design of antiviral compounds in the treatment of Acquired Immuno Deficiency Syndrome (AIDS). In this context, understanding the catalytic mechanism of the enzyme is of crucial importance as transition state structure directs inhibitor design. Most mechanistic proposals invoke nucleophilic attack on the scissile peptide bond by a water molecule. But such a water molecule coexisting with any ligand in the active site has not been found so far in the crystal structures. PRINCIPAL FINDINGS: We report here the first observation of the coexistence in the active site, of a water molecule WAT1, along with the carboxyl terminal product (Q product) peptide. The product peptide has been generated in situ through cleavage of the full-length substrate. The N-terminal product (P product) has diffused out and is replaced by a set of water molecules while the Q product is still held in the active site through hydrogen bonds. The position of WAT1, which hydrogen bonds to both the catalytic aspartates, is different from when there is no substrate bound in the active site. We propose WAT1 to be the position from where catalytic water attacks the scissile peptide bond. Comparison of structures of HIV-1 protease complexed with the same oligopeptide substrate, but at pH 2.0 and at pH 7.0 shows interesting changes in the conformation and hydrogen bonding interactions from the catalytic aspartates. CONCLUSIONS/SIGNIFICANCE: The structure is suggestive of the repositioning, during substrate binding, of the catalytic water for activation and subsequent nucleophilic attack. The structure could be a snap shot of the enzyme active site primed for the next round of catalysis. This structure further suggests that to achieve the goal of designing inhibitors mimicking the transition-state, the hydrogen-bonding pattern between WAT1 and the enzyme should be replicated.