1ASV

Avian sarcoma virus integrase catalytic core domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(1995) J.Mol.Biol. 253: 333-346

  • DOI: 10.1006/jmbi.1995.0556
  • Primary Citation of Related Structures:  1ASU, 1ASW

  • PubMed 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. ...

    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.


    Organizational Affiliation

    Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AVIAN SARCOMA VIRUS INTEGRASE
A
162Rous sarcoma virus (strain Schmidt-Ruppin B)Gene Names: gag-pro-pol
EC: 3.1.26.4, 3.1.-.-, 2.7.7.49, 2.7.7.7, 2.7.7.-, 3.4.23.-
Find proteins for O92956 (Rous sarcoma virus (strain Schmidt-Ruppin B))
Go to UniProtKB:  O92956
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCY
Query on OCY
A
L-PEPTIDE LINKINGC5 H11 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.550α = 90.00
b = 66.550β = 90.00
c = 80.870γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PROLSQrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-11-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance