User:Andrea Foote/Sandbox 1: Difference between revisions

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== Structure ==

[[Image:180429 proteopedia pura figures2.jpg|thumb|right|~~300px~~| A PUR domain is analogous to a left-handed handshake. PUR repeat I-II represented from [[5fgp]].]]

[[Image:180429 proteopedia pura figures2.jpg|thumb|right|400px| A PUR domain is analogous to a left-handed handshake. PUR repeat I-II represented from [[5fgp]].]]

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|~~300px~~| 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|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.

~~[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|left|500px| ([[5fgp]])]]~~

== Development ==

Purα expression is highest during fetal development, ~~specifically~~ in the brain, spinal cord~~, and genitalia~~. In humans and mice Purα expression ~~decreases~~ in adulthood, ~~and is restricted primarily to~~ the brain ~~and testes~~.

Purα expression is highest during fetal development, particularly in the brain and spinal cord. In humans and mice Purα expression is reduced in adulthood and, while still ubiquitous, levels are greatest in the brain.

== Tissue Specificity ==

@@ Line 7: / Line 7: @@
 == Structure ==
-[[Image:180429 proteopedia pura figures2.jpg|thumb|right|300px| A PUR domain is analogous to a left-handed handshake. PUR repeat I-II represented from [[5fgp]].]]
+[[Image:180429 proteopedia pura figures2.jpg|thumb|right|400px| A PUR domain is analogous to a left-handed handshake. PUR repeat I-II represented from [[5fgp]].]]
 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|300px| 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.
@@ Line 19: / Line 19: @@
 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|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.
-[[Image:180504 PurA Repeat 1 electron density.jpg|thumb|left|500px| ([[5fgp]])]]
 == Development ==
-Purα expression is highest during fetal development, specifically in the brain, spinal cord, and genitalia. In humans and mice Purα expression decreases in adulthood, and is restricted primarily to the brain and testes.
+Purα expression is highest during fetal development, particularly in the brain and spinal cord. In humans and mice Purα expression is reduced in adulthood and, while still ubiquitous, levels are greatest in the brain.
 == Tissue Specificity ==