Replication Termination Protein: Difference between revisions

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<scene name='Rtp_and_Tus_DNA_Binding/Wingdown/1'>Wing-down</scene>: Contacts with phosphate backbone of downstream DNA  
<scene name='Rtp_and_Tus_DNA_Binding/Wingdown/1'>Wing-down</scene>: Contacts with phosphate backbone of downstream DNA  
<Structure load='Lol1.pdb' size='400' color='white'/>




<scene name='Replication_Termination_Protein/Binding/1'>Residues binding to DNA</scene>
<scene name='Replication_Termination_Protein/Binding/1'>Residues binding to DNA</scene>


Residues binding in both RTP monomers: Gln15, Arg16, Leu35, Asn53, His54, Thr55, Tyr58, Arg59, His62, gln72 (RED)
Residues that bind in both monomers: Red
Residues binding in only wing down position: Lys14, Tyr33, Lys77, Gln83, Val86 (BLUE)
Residues binding in only wing up position: Thr9, Lys36, Glu56 (GREEN)


<Structure load='Lol1.pdb' size='400' color='white'/>
Residues that bind only in wing-up: Green
 
Residues that bind only in wing-down: Blue
 
{| class="wikitable"
|-
! 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)
|-
|}

Revision as of 04:35, 23 May 2011

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

Drag the structure with the mouse to rotate


Residues binding to 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)

Proteopedia Page Contributors and Editors (what is this?)

Craig Mooney, Michal Harel, Joel L. Sussman, Alexander Berchansky

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