User:Christina Manner/Sandbox 810: Difference between revisions

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The dimers AB and CD interact with each other via molecular interactions between B and C. Additionally, the palindromic sequence of the 'tra' box causes a base stacking between the beginning and the end of the sequence.

As A and B are differently elongated, there is a dimeric asymmetry that has two consequences for the function. At first, the <scene name='57/574296/N-ter_dimer/3'>N-terminal parts</scene> of the two monomers have different positions. The N-terminal part of A is between the ligand-binding domain and the DNA-binding domain in the center of the protein. In opposition to that, the N-terminal part of B is located externally. Moreover, there is a <scene name='57/574296/Neg_charged_dna_binding_region/2'>distribution of charge</scene> at the surface of the dimer. Because of that, the DNA-binding domain forms a long and basic region for the interaction with DNA, whereas the C-terminal residues form a positively charged patch exposed to the solvent. This region might be involved in protein-protein interaction with TraM <ref name = Volpari/>. TraM binds to TraR and prevents it from binding to the DNA and therefore prevents the activation of the transcription of the 'tra' genes <ref name = Volpari/>.

==='''Ligand ~~binding domain~~'''===

==='''Ligand Binding Domain'''===

The <scene name='57/574296/Ligand_binding_secondary/10'>ligand binding domain</scene> includes the residues 1 to 162. The ligand AAI is surrounded by three α-helices (α3, α4 and α5) and a five-stranded antiparallel β-sheet. The order of this β-sheet is 2-1-5-4-3.

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Following the ligand binding domain, the residues 163 to 175 form the <scene name='57/574296/Linker/3'>linker</scene> to the DNA binding domain. The residues 166 to 169 are disordered and cannot be seen in the structural model <ref name = Vannini/>.

==='''DNA ~~binding domain~~'''===

==='''DNA Binding Domain'''===

The DNA binding domain contains four <scene name='57/574296/Dna_binding_domain_alpha/1'> α-helices </scene> (α7, α8, α9, α10) and is provided by the C-terminal part of the protein by the residues 176 to 234. In monomer A or C, the first residues of α7, the last residues of α8 and the residues 232 to 234 form polar bonds with the N-terminal part of the ligand binding domain. In the B or D monomer, no such interactions were observed. Besides, helices α8 and α9 form the <scene name='57/574296/Hth/1'>HTH</scene> (Helix-Turn-Helix) motif <ref name = Vannini/>.

@@ Line 22: / Line 22: @@
 The dimers AB and CD interact with each other via molecular interactions between B and C. Additionally, the palindromic sequence of the 'tra' box causes a base stacking between the beginning and the end of the sequence.
 As A and B are differently elongated, there is a dimeric asymmetry that has two consequences for the function. At first, the <scene name='57/574296/N-ter_dimer/3'>N-terminal parts</scene> of the two monomers have different positions. The N-terminal part of A is between the ligand-binding domain and the DNA-binding domain in the center of the protein. In opposition to that, the N-terminal part of B is located externally. Moreover, there is a <scene name='57/574296/Neg_charged_dna_binding_region/2'>distribution of charge</scene> at the surface of the dimer. Because of that, the DNA-binding domain forms a long and basic region for the interaction with DNA, whereas the C-terminal residues form a positively charged patch exposed to the solvent. This region might be involved in protein-protein interaction with TraM <ref name = Volpari/>. TraM binds to TraR and prevents it from binding to the DNA and therefore prevents the activation of the transcription of the 'tra' genes <ref name = Volpari/>.
-==='''Ligand binding domain'''===
+==='''Ligand Binding Domain'''===
 The <scene name='57/574296/Ligand_binding_secondary/10'>ligand binding domain</scene> includes the residues 1 to 162. The ligand AAI is surrounded by three α-helices (α3, α4 and α5) and a five-stranded antiparallel β-sheet. The order of this β-sheet is 2-1-5-4-3.
@@ Line 29: / Line 30: @@
 Following the ligand binding domain, the residues 163 to 175 form the <scene name='57/574296/Linker/3'>linker</scene> to the DNA binding domain. The residues 166 to 169 are disordered and cannot be seen in the structural model <ref name = Vannini/>.
-==='''DNA binding domain'''===
+==='''DNA Binding Domain'''===
 The DNA binding domain contains four <scene name='57/574296/Dna_binding_domain_alpha/1'> α-helices </scene> (α7,  α8, α9,  α10) and is provided by the C-terminal part of the protein by the residues 176 to 234. In monomer A or C, the first residues of α7, the last residues of α8 and the residues 232 to 234 form polar bonds with the N-terminal part of the ligand binding domain. In the B or D monomer, no such interactions were observed. Besides, helices α8 and α9 form the <scene name='57/574296/Hth/1'>HTH</scene> (Helix-Turn-Helix) motif <ref name = Vannini/>.