Replication Termination Protein
Replication Termination Proteins
Rtp and Tus These polar fork bocking sites have been found in yeast, pea, frog and human genomes.
RTP
RTP is a DNA binding protein from Bacillus Subtilis that uses a helix-loop-helix binding motif. In solution it shows a symmetric structure typical of the winged helix loop helix family, with an unstructured N-terminus end, first alpha helix (a1), unstructured loop that is equivalent to the first beta sheet (B1), helix loop helix structure (a2-a3), 2 beta sheets with a connecting loop that makes up the 'wing' structure (B2 - B3) and an additional long alpha helix involved in dimerisation (a4).
Assymmetry of RTP in DNA-binding
Wing-up: Contacts upstream with rtp dimer bound to A-site
Wing-down: Contacts with phosphate backbone of downstream DNA
|
Residues that bind in both monomers: Red
Residues that bind only in wing-up: Green
Residues that bind only in wing-down: Blue
| Both monomers | Unit | Binding |
|---|---|---|
| Lys14 | Wing-down | Phosphate(13) |
| Gln15 | Both | Phosphate(14) |
| Arg16 | Both | Phosphate(13) |
| Tyr33 | Wing-down | Phosphate(3) |
| Leu35 | both | Phosphate(4) |
| Lys36 | Wing-up | Sugar(3) |
| Asn53 | Both | Phosphate(14) |
| His54 | Both | Guanine(5) |
| Thr55 | Both | Thymine(15) |
| Glu56 | Wing-up | Phosphate(13) |
| Tyr58 | Both | Phosphate(4/5) |
| Arg59 | Both | Guanine(14) |
| His62 | Both | Phosphate(5) |
| Gln72 | Both | Phosphate(5) |
| Lys77 | Wing-down | Phosphate(3) |
| Gln83 | Wing-down | Sugar(3) |
| Val86 | Wind-down | Phosphate(4) |
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