DNA and T-ag Sequences

<div><p>(A) The SV40 64-bp core-origin sequence. The pentanucleotides P1 through P4 are indicated above the sequence. Each GAGGC sequence is colored magenta, and its complement is cyan. The arrows indicate the 5′ → 3′ direction of the pentanucleotide sequence GAGGC. The AT-rich and early palindrome regions of the SV40 core origin are labeled.</p> <p>(B) The DNA duplex used in crystallization of the T-ag obd–DNA complex. This 21-mer contains the palindromic binding sites P1 and P3 and a mutated pentamer P2 site. The GAGGC sequences and their complements are indicated by magenta and cyan boxes, respectively. The altered P2 pentamer is indicated by hash-marks in magenta and cyan. As above, the arrows indicate the 5′ → 3′ direction of the pentanucleotide sequences, and the red X indicates that the P2 sequence is altered.</p> <p>(C) The BPV origin shows the E1 binding sites termed E1–1 through E1–4. The E1 binding sites are imperfect 5′-ATTGTT-3′ hexameric sequences. Boxes outline each binding site, and the binding sites are labeled. The arrows indicate the 5′ → 3′ direction of the binding site. The direct repeats (sites E1–1 and E1–2 or sites E1–3 and E1–4) overlap by 3 bp. The ATTGTT sequence (magenta) and its complement (cyan) are indicated. Lowercase letters are used for the portion of binding sites that do not overlap.</p> <p>(D) Structure-based sequence alignment of SV40 T-ag obd with BPV E1 obd. The secondary structure elements of the T-ag obd are shown above its amino acid sequence. Every tenth residue is indicated with a dot. T-ag obd residues that make base-specific contacts in the DNA co-structure are indicated by cyan boxes. T-ag obd residues that make phosphate interactions are indicated by red triangles above the amino acid sequence. There are two types of T-ag obd–obd interactions: the “head-to-head” type seen in the disulfide-linked dimer (possibly important in double-hexamer formation), and the “side-to-side” type (important in single-hexamer formation) seen in the spiral hexamer. T-ag obd residues that form the protein–protein interface in the disulfide-linked dimer structure are indicated by yellow boxes. T-ag obd residues that comprise the protein–protein interface in the spiral hexamer are indicated by an asterisk (*). Residues for BPV E1 obd that make base-specific contacts or phosphate contacts or participate in its dimer interface are indicated by pink boxes, magenta triangles below the E1 sequence, and green boxes, respectively. The information for E1 was obtained from the crystal structures of E1-obd with and without DNA.</p>