Sandbox Reserved 933: Difference between revisions

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== Structural Basis of LEAFY binding ==

[[Image:DNA_Recognition.jpg|~~400px~~|~~left~~|thumb| Figure 2. Site specific recognition of LFY protein at major (A) and minor (B) grooves. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. Red arrows marked site specific hydrogen bonds.]]

[[Image:DNA_Recognition.jpg|300px|right|thumb| Figure 2. Site specific recognition of LFY protein at major (A) and minor (B) grooves. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. Red arrows marked site specific hydrogen bonds.]]

=== General information about the structure ===

The ''LFY'' gene encodes a 424 amino acids protein that containing two domains. The N-terminal domain of LFY has been proved mediating homodimerization (ref) and it is also thought to be responsible for transcriptional activation <ref name="Weigel1992" /><ref name="Coen1990" />. The C-terminal consensus is highly conserved among land species and functioning as DNA-binding domain. Two DNA-protein binding structure for LEAFY were first published by Hame et al. 2008. These two structures include a recombinant C-terminal domain of LEAFY expressed by ''Escherichia coli'' strain RosettaBlue (DE3) and a short nucleotide structure from AP1 or AG promoter region. Final models of LFY-pAP1 and LFY-pAG were solved at 2.1 Å and 2.3 Å by X-ray diffraction and deposited as PDB entry <scene name='57/579703/2vy1/1'>2VY1</scene>/<scene name='57/579703/2vy2/1'>2VY2</scene>.

=== Site specific DNA recognition is conducted by a HTH-like motif ===

[[Image:Dimer_Bond.001.jpg|~~350px~~|right|thumb| Figure 3. Three residues mediate homodimerization of LFY dimerization at pAP1 site. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. ]]

[[Image:Dimer_Bond.001.jpg|300px|right|thumb| Figure 3. Three residues mediate homodimerization of LFY dimerization at pAP1 site. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. ]]

The general structure of LEAFY DNA binding domain consists 2 <scene name='57/579703/Beta-strand/1'>β strands</scene> at the beginning followed by 7 <scene name='57/579703/Alpha-helices_color/2'> α helices</scene>. A <scene name='57/579703/Alpha-helices_color/3'>helix-turn-helix</scene> (HTH) motif can be found between α2 and α3 helices, which is recruited to the <scene name='57/579703/Major_groove/2'>major groove </scene>of the binding DNA. There are two amino acid at this motif, <scene name='57/579703/Major_groove_asn291/1'>Asn 291</scene> on α2 and <scene name='57/579703/Major_groove_asn291/2'>Lys 307</scene> on α3 directly mediate site specific recognition with <scene name='57/579703/Major_groove_detail/1'>two guanines</scene> at the DNA strand. These two recognition sites were further validated by electrophoresis mobility shift assay (EMSA): mutation at either Asn 291 or Lys 307 dramatically decrease binding affinity to pAP1. In the minor groove, site specific recognition is conducted by <scene name='57/579703/Arg_237/1'>Arg 237</scene>, which is at the beginning of this structure. ''Arabidopsis'' intermediate mutant ''lfy-4'' (P240L) and ''lfy-5'' (T244M) were located near this site and validate the function ''in planta''<ref name="Weigel1992" />. The super position of specific recognition sites is summaries at figure 2.

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@@ Line 13: / Line 13: @@
 <StructureSection load='2VY1' size='400' side= 'right' caption='Structure of LFY binding with AP1 and AG promoter region (PDB entry: 2VY1/2VY2)'  Scene=57/579703/2vy1/1>
 == Structural Basis of LEAFY binding ==
-[[Image:DNA_Recognition.jpg|400px|left|thumb| Figure 2. Site specific recognition of LFY protein at major (A) and minor (B) grooves. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. Red arrows marked site specific hydrogen bonds.]]
+[[Image:DNA_Recognition.jpg|300px|right|thumb| Figure 2. Site specific recognition of LFY protein at major (A) and minor (B) grooves. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. Red arrows marked site specific hydrogen bonds.]]
 === General information about the structure ===
 The ''LFY'' gene encodes a 424 amino acids protein that containing two domains. The N-terminal domain of LFY has been proved mediating homodimerization (ref) and it is also thought to be responsible for   transcriptional activation <ref name="Weigel1992" /><ref name="Coen1990" />. The C-terminal consensus is highly conserved among land species and functioning as DNA-binding domain. Two DNA-protein binding structure for LEAFY were first published by Hame et al.  2008. These two structures include a recombinant C-terminal domain of LEAFY expressed by ''Escherichia coli'' strain RosettaBlue (DE3) and a short nucleotide structure from AP1 or AG promoter region. Final models of LFY-pAP1 and LFY-pAG were solved at 2.1 Å and 2.3 Å by X-ray diffraction and deposited as PDB entry <scene name='57/579703/2vy1/1'>2VY1</scene>/<scene name='57/579703/2vy2/1'>2VY2</scene>.
 === Site specific DNA recognition is conducted by a HTH-like motif ===
-[[Image:Dimer_Bond.001.jpg|350px|right|thumb| Figure 3. Three residues mediate homodimerization of LFY dimerization at pAP1 site. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. ]]
+[[Image:Dimer_Bond.001.jpg|300px|right|thumb| Figure 3. Three residues mediate homodimerization of LFY dimerization at pAP1 site. Assembly of PDB entry 2VY1 were obtained from PISA server and further visualized by Pymol. ]]
 The general structure of LEAFY DNA binding domain consists 2 <scene name='57/579703/Beta-strand/1'>β strands</scene> at the beginning followed by 7 <scene name='57/579703/Alpha-helices_color/2'> α helices</scene>. A <scene name='57/579703/Alpha-helices_color/3'>helix-turn-helix</scene> (HTH) motif can be found between α2 and  α3 helices, which is recruited to the <scene name='57/579703/Major_groove/2'>major groove </scene>of the binding DNA. There are two amino acid at this motif, <scene name='57/579703/Major_groove_asn291/1'>Asn 291</scene> on α2 and <scene name='57/579703/Major_groove_asn291/2'>Lys 307</scene> on α3 directly mediate site specific recognition with <scene name='57/579703/Major_groove_detail/1'>two guanines</scene> at the DNA strand. These two recognition sites were further validated by electrophoresis mobility shift assay (EMSA): mutation at either Asn 291 or Lys 307 dramatically decrease binding affinity to pAP1. In the minor groove, site specific recognition is conducted by <scene name='57/579703/Arg_237/1'>Arg 237</scene>, which is at the beginning of this structure. ''Arabidopsis'' intermediate mutant ''lfy-4'' (P240L) and ''lfy-5'' (T244M) were located near this site and validate the function ''in planta''<ref name="Weigel1992" />. The super position of specific recognition sites is summaries at figure 2.