PDBsum entry 1b9f

Transferase

PDB id: 1b9f

Contents

Protein chain

151 a.a. *

Ligands

CAC ×2

SO4

Waters ×69

* Residue conservation analysis

PDB id:

1b9f

Name:

Transferase

Title:

Mobility of an HIV-1 integrase active site loop is correlated with catalytic activity

Structure:

Protein (integrase). Chain: a. Fragment: catalytic core domain. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus type 1 (clone 12). Organism_taxid: 11679. Strain: 1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.

Biol. unit:

Monomer (from PDB file)

Resolution:

1.70Å R-factor: 0.243 R-free: 0.280

Authors:

J.Greenwald,V.Le,S.L.Butler,F.D.Bushman,S.Choe

Key ref:

J.Greenwald et al. (1999). The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity. Biochemistry, 38, 8892-8898. PubMed id: 10413462 DOI: 10.1021/bi9907173

Date:

11-Feb-99 Release date: 19-Jul-99

Protein chain

P12497  (POL_HV1N5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate NY5)

Seq: 1435 a.a.

Struc: 151 a.a.*

* PDB and UniProt seqs differ at 3 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: 10.1021/bi9907173

Biochemistry 38:8892-8898 (1999)

PubMed id: 10413462

The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.

J.Greenwald, V.Le, S.L.Butler, F.D.Bushman, S.Choe.

ABSTRACT

Replication of HIV-1 requires the covalent integration of the viral cDNA into the host chromosomal DNA directed by the virus-encoded integrase protein. Here we explore the importance of a protein surface loop near the integrase active site using protein engineering and X-ray crystallography. We have redetermined the structure of the integrase catalytic domain (residues 50-212) using an independent phase set at 1.7 A resolution. The structure extends helix alpha4 on its N-terminal side (residues 149-154), thus defining the position of the three conserved active site residues. Evident in this and in previous structures is a conformationally flexible loop composed of residues 141-148. To probe the role of flexibility in this loop, we replaced Gly 140 and Gly 149, residues that appear to act as conformational hinges, with Ala residues. X-ray structures of the catalytic domain mutants G149A and G140A/G149A show further rigidity of alpha4 and the adjoining loop. Activity assays in vitro revealed that these mutants are impaired in catalysis. The DNA binding affinity, however, is minimally affected by these mutants as assayed by UV cross-linking. We propose that the conformational flexibility of this active site loop is important for a postbinding catalytic step.