Structure of a DNA unwinding protein and its complexes with oligodeoxynucleotides by X-ray diffraction

Journal Article · Wed Oct 01 00:00:00 EDT 1980 · Biophys. J.; (United States)

DOI:https://doi.org/10.1016/S0006-3495(80)84931-9· OSTI ID:6761356

McPherson, A ^[1]; Jurnak, F; Wang, A; Kolpak, F; Rich, A; Molineux, I; Fitzgerald, P

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1. Univ. of California, Riverside

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 1.3 A resolution by x-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The cleft then acts as an elongated pair of jaws that draws the DNA between them by charge interactions involving the phosphates with the interior lysines an arginines. The jaws then close on the DNA strand through small conformation changes and the rotation of aromatic side-chains into position to stack upon the purines and pyrimidines. Complexes of the gene 5 protein with a variety of oligodeoxynucleotides have been formed and crystallized for x-ray diffraction analysis. The crystallographic parameters of four different unit cells indicate that the fundamental unit of the complex is composed of six gene 5 protein dimers. We believe this aggregate has 622 point group symmetry and is a ring formed by end to end closure of a linear array of six dimers. From our results we have proposed a double helical model for the gene 5 protein-DNA complex in which the protein forms a spindle or core around which the DNA is spooled. 5.0-A x-ray diffraction data from one of the crystalline complexes is currently being analyzed by molecular replacement techniques to obtain what we believe will be the first direct visualization of a protein-deoxyribonucleic acid complex approaching atomic resolution.

• OSTI ID: 6761356
• Journal Information: Biophys. J.; (United States), Vol. 32:1
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DNA
CONFIGURATION INTERACTION
NUCLEOPROTEINS
STRUCTURAL CHEMICAL ANALYSIS
NUCLEOTIDES
BACTERIOPHAGES
BIOCHEMISTRY
BIOPHYSICS
COMPLEXES
HELICAL CONFIGURATION
MOLECULAR BIOLOGY
MOLECULAR STRUCTURE
SPATIAL DEPENDENCE
X-RAY DIFFRACTION
CHEMISTRY
COHERENT SCATTERING
CONFIGURATION
DIFFRACTION
MICROORGANISMS
NUCLEIC ACIDS
ORGANIC COMPOUNDS
PARASITES
PROTEINS
SCATTERING
VIRUSES
550200* - Biochemistry