PDBsum entry 1asu

DNA integration

PDB id: 1asu

Contents

Protein chain

162 a.a. *

Ligands

EPE

Waters ×181

* Residue conservation analysis

PDB id:

1asu

Name:

DNA integration

Title:

Avian sarcoma virus integrase catalytic core domain crystallized from 2% peg 400, 2m ammonium sulfate, hepes ph 7.5

Structure:

Avian sarcoma virus integrase. Chain: a. Engineered: yes. Mutation: yes. Other_details: crystallized from 2% peg 400, 2m ammonium sulfate, hepes ph 7.5

Source:

Avian sarcoma virus. Organism_taxid: 11876. Strain: schmidt-ruppin b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.70Å R-factor: 0.152 R-free: 0.188

Authors:

G.Bujacz,M.Jaskolski,J.Alexandratos,A.Wlodawer

Key ref:

G.Bujacz et al. (1995). High-resolution structure of the catalytic domain of avian sarcoma virus integrase. J Mol Biol, 253, 333-346. PubMed id: 7563093 DOI: 10.1006/jmbi.1995.0556

Date:

25-Aug-95 Release date: 14-Nov-95

Protein chain

O92956  (POL_RSVSB) -  Gag-Pol polyprotein from Rous sarcoma virus subgroup B (strain Schmidt-Ruppin)

Seq: 1603 a.a.

Struc: 162 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.- - ?????
• Enzyme class 3: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: E.C.3.1.-.-
• Enzyme class 6: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: E.C.3.4.23.- - ?????

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: 10.1006/jmbi.1995.0556

J Mol Biol 253:333-346 (1995)

PubMed id: 7563093

High-resolution structure of the catalytic domain of avian sarcoma virus integrase.

G.Bujacz, M.Jaskólski, J.Alexandratos, A.Wlodawer, G.Merkel, R.A.Katz, A.M.Skalka.

ABSTRACT

Retroviral integrase (IN) functions to insert retroviral DNA into the host cell chromosome in a highly coordinated manner. IN catalyzes two biochemically separable reactions: processing of the viral DNA ends and joining of these ends to the host DNA. Previous studies suggested that these two reactions are chemically similar and are carried out by a single active site that is characterized by a highly conserved constellation of carboxylate residues, the D,D(35)E motif. We report here the crystal structure of the isolated catalytic domain of avian sarcoma virus (ASV) IN, solved using multiwavelength anomalous diffraction data for a selenomethionine derivative and refined at 1.7 A resolution. The protein is a crystallographic dimer with each monomer featuring a five-stranded mixed beta-sheet region surrounded by five alpha-helices. Based on the general fold and the arrangement of catalytic carboxylate residues, it is apparent that ASV IN is a member of a superfamily of proteins that also includes two types of nucleases, RuvC and RNase H. The general fold and the dimer interface are similar to those of the analogous domain of HIV-1 IN, whose crystal structure has been determined at 2.5 A resolution. However, the ASV IN structure is more complete in that all three critical carboxylic acids, Asp64, Asp121 and Glu157, are ordered. The ordered active site and the considerably higher resolution of the present structure are all important to an understanding of the mechanism of retroviral DNA integration, as well as for designing antiviral agents that may be effective against HIV.

Selected figure(s)

Figure 1.
Figure 1. Primary structure of retroviral integrase. A, Representation of ASV IN showing the three functional domains and indicating the fragment included in the domain analyzed in this investigation. B, Alignment of the amino acid sequences in the ASV andHIV-1IN catalytic domains, with the elements of secondary structure indicated. Residues shown in red are identical, those shown in blue are of similar type. The sequence with a broken underline was not observed in the crystal structure of HIV-1 IN.

Figure 5.
Figure 5. Stereoviews of the dimers of the catalytic domain of IN generated using O (Jones & Kjeldgaard, 1994). A, A dimer of the ASV IN core domain viewed along its 2-fold axis, with Wat450 positions marked as blue spheres. B, Superposition of the main chains of ASV and HIV-1 IN core domains. The superposition is based on the best fit between the C a atoms of the blue (ASV) and gold (HIV-1) chains. The green (ASV) and red (HIV-1) subunits (generated by the corresponding molecular dyads) show considerable deviations.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1995, 253, 333-346) copyright 1995.

Figures were selected by an automated process.