NORMAL GENOMIC

• Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K
• Crystal structure of an archaeal intein-encoded homing endonucleasePI-PfuI.
• J Mol Biol. 2000; 300: 889-901
• Display abstract

• Inteins possess two different enzymatic activities, self-catalyzed proteinsplicing and site-specific DNA cleavage. These endonucleases, which areclassified as part of the homing endonuclease family, initiate themobility of their genetic elements into homologous alleles. They recognizelong asymmetric nucleotide sequences and cleave both DNA strands in amonomer form. We present here the 2.1 A crystal structure of the archaealPI-PfuI intein from Pyroccocus furiosus. The structure reveals a uniquedomain, designated here as the Stirrup domain, which is inserted betweenthe Hint domain and an endonuclease domain. The horseshoe-shaped Hintdomain contains a catalytic center for protein splicing, which involvesboth N and C-terminal residues. The endonuclease domain, which is insertedinto the Hint domain, consists of two copies of substructure related by aninternal pseudo 2-fold axis. In contrast with the I-CreI homingendonuclease, PI-PfuI possibly has two asymmetric catalytic sites at thecenter of a putative DNA-binding cleft formed by a pair of four-strandedbeta-sheets. DNase I footprinting experiments showed that PI-PfuI coversmore than 30 bp of the substrate asymmetrically across the cleavage site.A docking model of the DNA-enzyme complex suggests that the endonucleasedomain covers the 20 bp DNA duplex encompassing the cleavage site, whereasthe Stirrup domain could make an additional contact with another upstream10 bp region. For the double-strand break, the two strands in the DNAduplex were cleaved by PI-PfuI with different efficiencies. We suggestthat the cleavage of each strand is catalyzed by each of the twonon-equivalent active sites.

• McPherson A, Jurnak F, Wang A, Molineux I, Rich A
• Structure of the DNA binding cleft of the gene 5 protein frombacteriophage fd.
• J Supramol Struct. 1979; 10: 457-65
• Display abstract

• The structure of the gene 5 DNA unwinding protein from bacteriophage fdhas been solved to 2.3-A resolution by X-ray diffraction techniques. Themolecule contains an extensive cleft region that we have identified as theDNA 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 acidresidues that serve to draw the polynucleotide backbone into the cleft.Arrayed along the external edges of the groove are a number of aromaticamino acid side groups that are in position to stack upon the bases of theDNA and fix it in place. The structure and binding mechanism as wevisualize it appear to be fully consistent with evidence provided byphysical-chemical studies of the protein in solution.

• Schmitz KS
• Cooperative monomer binding by polynucleotides. Effect of multiple-loopconfigurations on formation of triple-stranded complexes.
• Biopolymers. 1974; 13: 1039-53

• Arnott S, Wilkins MH, Fuller W, Langridge R
• Molecular and crystal structures of double-helical RNA. 3. An 11-foldmolecular model and comparison of the agreement between the observed andcalculated three-dimensional diffraction data for 10- and 11-fold models.
• J Mol Biol. 1967; 27: 535-48

• Tsuboi M, Iitaka Y, Mitsui Y, Matsuo K, Fuse Y
• Molecular structures of double helical DNA and RNA.
• Jpn J Med Sci Biol. 1967; 20: 252-252

• Hijmans J
• Theory of the helix-coil transition for synthetic polynucleotides formingbranched helical structures.
• J Chem Phys. 1967; 47: 5116-28