User:Andrea Foote/Sandbox 1: Difference between revisions

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Purα functions as a dimer composed of two intramolecular domains and one intermolecular domain. The Purα monomer contains three semi-conserved repeated amino acid sequences, named in order from N->C: PUR repeats I, II, and III. These repeats fold to form two domains: <scene name='78/786627/5fgp_intro/9'>PUR repeats I and II</scene> associating to form the I-II domain or “intramolecular domain”, while <scene name='78/786627/5fgo_repeatiii/3'>PUR repeat III</scene> facilitates dimerization through association with a repeat III from a second Purα monomer or repeat III of Purβ, forming an "intermolecular domain". Each PUR repeat is connected by a flexible linker region of 10-20 amino acids, depending on the species, linker and algorithm used to determine repeats. Each PUR repeat contains a beta-sheet composed of four beta-strands, followed by a single alpha-helix. While Purα is not yet officially classified by SCOP or CATH, its structure is that of an α+β protein.

[[Image:180503 PurA Why2 ~~comparison~~.jpg|thumb|right|~~400px~~| PUR domains are structurally similar to the fold in Whirly proteins. Left: PUR repeat I-II ([[5fgp]]), right: WHY2 ([[3n1k]]).]]

[[Image:180503 PurA Why2 comparison1.jpg|thumb|right|350px| PUR domains are structurally similar to the fold in Whirly proteins. Left: PUR repeat I-II ([[5fgp]]), right: WHY2 ([[3n1k]]).]]

The domains of Purα have been described as "Whirly-like" folds because of their structural similarity to the DNA-binding Whirly class of proteins found in plants.<ref>PMID:19846792</ref> Whirlys are also ssDNA binding proteins, however unlike PUR family proteins they are not sequence-specific.

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PurA has also been shown to enhance expression of myelin basic protein (MBP) in developing mouse brain tissue through its binding to an MB1 regulatory motif -15 to -40 nucleotides upstream of the transcription start site. MBP is an important protein found in myelin sheaths of the central nervous system.<ref>PMID:7657701</ref>

[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|right|~~300px~~|PUR repeat I electron density map showing base stacking between Y57 and guanine. The DNA strand present in this electron density map was omitted from the [[5fgp]] PDB file but is shown in the original publication (Weber, J. et al., 2016, eLIFE).<ref>PMID:26744780</ref> ([[5fgp]])]]

[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|right|350px|PUR repeat I electron density map showing base stacking between Y57 and guanine. The DNA strand present in this electron density map was omitted from the [[5fgp]] PDB file but is shown in the original publication (Weber, J. et al., 2016, eLIFE).<ref>PMID:26744780</ref> ([[5fgp]])]]

High-affinity nucleic acid-binding function is dependent on Purα dimerization. Purα forms homodimers in addition to heterodimers with Purβ. PurA is known to repress various genes including SMαA.

<scene name='78/786627/5fgp_57and145/1'>Two aromatic residues spatially conserved on PUR repeats I and II</scene>, Y57 (repeat I) and F145 (repeat II), located on the solvent-exposed surface of the beta-sheets, contribute to the DNA unwinding activity of Purα through base stacking interactions with DNA bases.<ref>PMID:26744780</ref> Although not shown in the [[5fgp]] PDB file, Y57 interacts with a second strand of DNA via base stacking interactions with guanine. It was presumably omitted because repeat I has significantly less affinity for purine-rich DNA than does repeat II, and it is believed that most of the DNA binding and unwinding activity occurs via interactions of DNA with the beta-sheet of repeat II.<ref>PMID:26744780</ref> <scene name='78/786627/5fgo_repeatiii/4'>PUR repeat III also has an aromatic residue at this location (Y219)</scene> that could undergo base-stacking interactions with DNA, however Weber, et al. observed negligible unwinding activity in this repeat.<ref>PMID:26744780</ref> Furthermore, this group found repeat III to bind ssDNA with significantly less (~30-fold less) affinity than repeat I-II.

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 Purα functions as a dimer composed of two intramolecular domains and one intermolecular domain. The Purα monomer contains three semi-conserved repeated amino acid sequences, named in order from N->C: PUR repeats I, II, and III. These repeats fold to form two domains: <scene name='78/786627/5fgp_intro/9'>PUR repeats I and II</scene> associating to form the I-II domain or “intramolecular domain”, while <scene name='78/786627/5fgo_repeatiii/3'>PUR repeat III</scene> facilitates dimerization through association with a repeat III from a second Purα monomer or repeat III of Purβ, forming an "intermolecular domain". Each PUR repeat is connected by a flexible linker region of 10-20 amino acids, depending on the species, linker and algorithm used to determine repeats. Each PUR repeat contains a beta-sheet composed of four beta-strands, followed by a single alpha-helix. While Purα is not yet officially classified by SCOP or CATH, its structure is that of an α+β protein.
-[[Image:180503 PurA Why2 comparison.jpg|thumb|right|400px| PUR domains are structurally similar to the fold in Whirly proteins. Left: PUR repeat I-II ([[5fgp]]), right: WHY2 ([[3n1k]]).]]
+[[Image:180503 PurA Why2 comparison1.jpg|thumb|right|350px| PUR domains are structurally similar to the fold in Whirly proteins. Left: PUR repeat I-II ([[5fgp]]), right: WHY2 ([[3n1k]]).]]
 The domains of Purα have been described as "Whirly-like" folds because of their structural similarity to the DNA-binding Whirly class of proteins found in plants.<ref>PMID:19846792</ref> Whirlys are also ssDNA binding proteins, however unlike PUR family proteins they are not sequence-specific.
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 PurA has also been shown to enhance expression of myelin basic protein (MBP) in developing mouse brain tissue through its binding to an MB1 regulatory motif -15 to -40 nucleotides upstream of the transcription start site. MBP is an important protein found in myelin sheaths of the central nervous system.<ref>PMID:7657701</ref>
-[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|right|300px|PUR repeat I electron density map showing base stacking between Y57 and guanine. The DNA strand present in this electron density map was omitted from the [[5fgp]] PDB file but is shown in the original publication (Weber, J. et al., 2016, eLIFE).<ref>PMID:26744780</ref> ([[5fgp]])]]
+[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|right|350px|PUR repeat I electron density map showing base stacking between Y57 and guanine. The DNA strand present in this electron density map was omitted from the [[5fgp]] PDB file but is shown in the original publication (Weber, J. et al., 2016, eLIFE).<ref>PMID:26744780</ref> ([[5fgp]])]]
 High-affinity nucleic acid-binding function is dependent on Purα dimerization. Purα forms homodimers in addition to heterodimers with Purβ. PurA is known to repress various genes including SMαA.
 <scene name='78/786627/5fgp_57and145/1'>Two aromatic residues spatially conserved on PUR repeats I and II</scene>, Y57 (repeat I) and F145 (repeat II), located on the solvent-exposed surface of the beta-sheets, contribute to the DNA unwinding activity of Purα through base stacking interactions with DNA bases.<ref>PMID:26744780</ref> Although not shown in the [[5fgp]] PDB file, Y57 interacts with a second strand of DNA via base stacking interactions with guanine. It was presumably omitted because repeat I has significantly less affinity for purine-rich DNA than does repeat II, and it is believed that most of the DNA binding and unwinding activity occurs via interactions of DNA with the beta-sheet of repeat II.<ref>PMID:26744780</ref> <scene name='78/786627/5fgo_repeatiii/4'>PUR repeat III also has an aromatic residue at this location (Y219)</scene> that could undergo base-stacking interactions with DNA, however Weber, et al. observed negligible unwinding activity in this repeat.<ref>PMID:26744780</ref> Furthermore, this group found repeat III to bind ssDNA with significantly less (~30-fold less) affinity than repeat I-II.