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==Purine-rich element binding protein alpha==

== Introduction ==

'''Purine-rich element binding protein alpha (Purα)''' is a transcription factor with a molecular weight of ~35 kDa encoded by the PURA gene. It possesses ATP-independent dsDNA unwinding activity, and is known to bind sequence-specific purine-rich regions of ssDNA and ssRNA, recognizing GGN motifs. Purα is a member of the PUR family of proteins, which includes Purβ and two isoforms of Purγ. In its functional dimeric form Purα is known to repress expression of smooth muscle alpha actin (SMαA) encoded by the ''Acta2'' gene. It is also known to be involved in DNA replication and cell cycle regulation as well as mRNA translation. It plays a crucial role in nervous system development, and ~~mutations in Purα have~~ been implicated in two neurological diseases: PURA syndrome and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) (see Disease section).<ref>PMID:26744780</ref>

'''Purine-rich element binding protein alpha (Purα)''' is a transcription factor with a molecular weight of ~35 kDa encoded by the ''PURA'' gene. It possesses ATP-independent dsDNA unwinding activity, and is known to bind sequence-specific purine-rich regions of ssDNA and ssRNA, recognizing GGN motifs. Purα is a member of the PUR family of proteins, which includes Purβ and two isoforms of Purγ. In its functional dimeric form Purα is known to repress expression of smooth muscle alpha actin (SMαA) encoded by the ''Acta2'' gene. It is also known to be involved in DNA replication and cell cycle regulation, as well as mRNA translation. It plays a crucial role in nervous system development, and has been implicated in two neurological diseases: PURA syndrome and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) (see Disease section).<ref>PMID:26744780</ref>

[[Image:180503 PurA dimer.jpg|thumb|center|700px| Artist representation of a Purα homodimer (linkers between repeats I-II and III (red) were drawn in PowerPoint and are NOT to scale). NOTE: This is NOT a verified model, but a rough placement to show all three repeats together. It is not known what the orientation of these domains are relative to one another. (Repeat I-II ([[5fgp]]): purple (I) and orange (II), repeat III ([[5fgo]]): cyan).]]

== 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/2'>PUR repeat III</scene> facilitates dimerization through association with a repeat III from a second Purα monomer or repeat III of Purβ. Each PUR repeat is connected by flexible linker ~~regions~~. 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.

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 ~~Purα~~ they are not sequence-specific.

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.

The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA ~~conjugation~~ are: <scene name='78/786627/Repeati_resi/2'>(repeat I) Q52, S53 and K54</scene>; <scene name='78/786627/Repeatii_resi/1'>(repeat II) K138, N140, R142, and F145</scene>. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the ~~following~~ cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>

The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues indicated by this crystal structure to be involved in protein-DNA binding are: <scene name='78/786627/Repeati_resi/3'>(repeat I) Q52, S53 and K54</scene>; <scene name='78/786627/Repeatii_resi/1'>(repeat II) K138, N140, R142, and F145</scene>. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 in repeat II of the protein. This <scene name='78/786627/5fgp_57and145/3'>phenylalanine-guanine stacking interaction</scene> disrupts base-stacking within the DNA resulting in the neighboring cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity by EMSA using a F145 mutant.<ref>PMID:26744780</ref>

== Function ==

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

Purα binds to single stranded purine-rich regions of DNA or RNA. In particular, Purα (and Purβ) are known to bind the purine-rich tract containing an MCAT enhancer motif in the 5’ region of the sense strand of the smooth muscle alpha actin gene (''Acta2''). Purα functions as a repressor at both transcriptional and translational levels. At the level of transcription Purα (and Purβ) act in concert with Y-box-binding protein 1 (YB-1 in humans or MSY1 in mice) which binds the antisense pyrimidine-rich strand, together acting to repress ''Acta2'' expression. At the level of translation Purα, Purβ and MSY-1 (YB-1 in humans) have been shown to bind a region in exon 3 of ''Acta2'' mRNA that is structurally similar to the MCAT (AGGAATG) enhancer element and prevent transcription in fibroblasts.<ref>PMID:10608902</ref>

<scene name='78/786627/5fgp_57and145/1'>Two aromatic residues</scene>, Y57 (repeat I) and F145 (repeat II) ~~have been implicated~~ in the DNA unwinding activity of ~~PurA~~.<ref>PMID:26744780</ref>

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.

== 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 ==

While Purα is a ubiquitously expressed protein in all cell types, it is generally found at low levels in most tissues. However, in adult humans and mice Purα expression is highest in the brain and spinal cord, and to a lesser extent in the testes. Purα has been shown to be upregulated in cardiac myocyte gap junctions following heart transplant in mice, colocalizing with SMαA.<ref>PMID:18344281</ref>

== Interactions ==

Purα is known to interact with:

*Purβ

*Serum response factor (SRF)

*Sp1<ref>PMID:10457364</ref>

*E2F-1<ref>PMID:10597240</ref>

*Y-box-binding protein 1 (YB-1) (MSY1 in mice)<ref>PMID:10082537</ref>

*Retinoblastoma protein (Rb)<ref>PMID:7592647</ref>

*Rm62 RNA helicase (''Drosophila''), p68 RNA helicase (mammalian)<ref>PMID:21655086</ref>

*JCV T-antigen<ref>PMID:8943069</ref>

*Cyclin A/Cdk2 (PurA binds to the Cdk2 moiety)<ref>PMID:15707957</ref>

== Disease ==

Mutations in the ''PURA'' gene resulting in haploinsufficiency ~~of Purα~~ are known to cause the neurological disease PURA syndrome. PURA syndrome appears early in development, , with patients exhibiting severe developmental delay, seizures, feeding difficulty, ~~of severe~~ intellectual disabilities~~, movements~~, vision, hypotonia, premature ~~telarche, . This disease has no cure, and life expectancy is~~ .<ref>PMID:29097605</ref>. Purα knock-out mice exhibit similar neurological symptoms such as severe tremor developing at about postnatal week two, and feeding difficulties. These mice die after approximately one month. Heterozygous mice display less severe symptoms including seizures upon handling. <ref>PMID:25342064</ref>

Mutations in the ''PURA'' gene resulting in haploinsufficiency are known to cause the neurological disease PURA syndrome, which has no cure. PURA syndrome appears early in development, with patients exhibiting severe developmental delay, seizures, feeding difficulty, intellectual disabilities, vision problems, hypotonia, and premature thelarche.<ref>PMID:29097605</ref> Purα knock-out mice exhibit similar neurological symptoms such as severe tremor developing at about postnatal week two, and feeding difficulties. These mice die after approximately one month. Heterozygous mice display less severe symptoms including seizures upon handling. <ref>PMID:25342064</ref> Interestingly, to date there have been no published accounts of phenotypic abnormalities in humans or mice with mutations in Purβ.

Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is another disease associated with abnormal activity of Purα. In 2006, Johnson et al. observed that Purα colocalized with Fragile-X Mental Retardation Protein (FMRP) in mouse neuronal dendrites.<ref>PMID:16436378</ref> Purα also was found to be involved in dendritic mRNA transport, and in a ''Drosophila'' model of Fragile-X Tremor/Ataxia Syndrome it was hypothesized that the overexpression of ''FMR1'' mRNA (encoding FMRP) resulted in Purα being bound to these mRNAs leading to the apparent deficiency in Purα activity and accumulation of RNA-protein inclusion bodies resulting in FXTAS symptoms.<ref>PMID:17698009</ref><ref>PMID:21655086</ref>

== The Storybook Version of Pur Protein History (Just for Fun!) ==

In a lab across from central park in Manhattan, Edward Johnson and his postdoctoral fellow Andrew Bergemann stumbled on a protein in 1991 that would in years to come open doors to understanding diseases of neurological and cardiovascular origin. They named the protein Pur (pronounced “purr”) after its ability to bind a sequence of bent DNA rich in As and Gs, or purine nucleotides, called the “PUR element.” This region of DNA, found near the origin of replication, was thought to be involved in the regulation of DNA replication.<ref>PMID:1545807</ref> At the time, no sequence-specific single-stranded DNA binding proteins were known to exist. The novelty of the findings were tremendous, and paved the way for many future studies of sequence-specific DNA-binding proteins.

While the focus of Johnson and Bergemann’s research was in DNA replication in cancer and AIDS, in the years that followed their discovery, Pur was found to interact with a tumor suppressor “retinoblastoma protein” or Rb. Likely as a result of funding available in cancer research and Rb, research has shifted from Pur’s role in DNA replication toward instead, its capacity to regulate transcription and translation, or the cellular processes involved in building proteins.

In 1992, Bergemann, Johnson and Ma found what appeared to be a cousin of Pur. With only a C-terminal sequence to work from, the protein appeared to be similar but not identical to Pur. They named the putative protein “Purβ” and from then on referred to the original Pur protein as Purα.<ref>PMID:1448097</ref> Shortly thereafter in 1997, Kelm, et al. working to deduce the sequence of a protein they termed “vascular actin single-stranded DNA binding factor 2” (VACssBF2), isolated two different proteins of identical molecular weight to Purα and the putative Purβ. Upon sequencing and cloning of isolated cDNA, the team published the first full length sequence of what is now known to be Purβ.<ref>PMID:9334258</ref> Since this time, in humans three splice variants have been found of Purα, one of Purβ and two isoforms of another Pur family member Purγ: Purγ-A and Purγ-B.

Purγ has been studied to a far lesser degree than Purα and Purβ. While little is yet known about the actions of the Purγ protein, Johnson and Liu in 2002 found that the Purγ-A isoform mRNA was expressed at very low levels or not at all in normal human tissues, but highly expressed in a panel of cancer cell types.<ref>PMID:12034829</ref> Similarly, Purγ-B mRNA was absent in human tissues except the testes, and in several tumor tissue types. Most of the research surrounding the Pur family of proteins has focused on Purα due to its involvement in neurological disorders, however interest in Purβ has increased in recent years as it has been implicated in cardiovascular disease, fibrosis and acute myelogenous leukemia.<ref>PMID:27064749</ref>

== 3D Structures of Purα ==

*[[5fgp]] (I-II repeat complex with DNA. ''Drosophila m.'')<ref>PMID:19846792</ref>

*[[5fgo]] (III repeat dimer. ''Drosophila m.'')<ref>PMID:26744780</ref>

*[[3k44]] (I-II repeat, apo. ''Drosophila m.'')<ref>PMID:26744780</ref>

*[[3nm7]] (Apo. ''Borrelia b.'' Note: the ''Borrelia'' homolog of Purα contains only one PUR repeat)<ref>PMID:20976240</ref>

*[[3n8b]] (Apo. ''Borrelia b.'' Note: the ''Borrelia'' homolog of Purα contains only one PUR repeat)<ref>PMID:20976240</ref>

~~Fragile X-associated Tremor~~/~~Ataxia Syndrome (FXTAS) is another disease associated with abnormal activity of Purα~~. Normally between __ and __ copies of __ , however in greater than __ copies can result in ___ causing delayed-onset neurological problems. FXTAS generally develops in middle age, and is characterized by tremor, ataxia, and ___.

== Additional Resources ==

For more information on PURA syndrome, visit the PURA Syndrome Foundation website: [https://www.purasyndrome.org]

JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>

This page was created using JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>

== References ==

@@ Line 1: / Line 1: @@
 ==Purine-rich element binding protein alpha==
 <StructureSection load='5fgp' size='340' side='right' caption='''Drosophila Purα intramolecular domain (purple: PUR repeat I, orange: PUR repeat II) in complex with DNA (green). X-ray diffraction, 2Å resolution ([[5fgp]]).''' scene='78/786627/5fgp_intro/9'>
 == Introduction ==
-'''Purine-rich element binding protein alpha (Purα)'''  is a transcription factor with a molecular weight of ~35 kDa encoded by the PURA gene. It possesses ATP-independent dsDNA unwinding activity, and is known to bind sequence-specific purine-rich regions of ssDNA and ssRNA, recognizing GGN motifs. Purα is a member of the PUR family of proteins, which includes Purβ and two isoforms of Purγ. In its functional dimeric form Purα is known to repress expression of smooth muscle alpha actin (SMαA) encoded by the ''Acta2'' gene. It is also known to be involved in DNA replication and cell cycle regulation as well as mRNA translation. It plays a crucial role in nervous system development, and mutations in Purα have been implicated in two neurological diseases: PURA syndrome and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) (see Disease section).<ref>PMID:26744780</ref>
+'''Purine-rich element binding protein alpha (Purα)'''  is a transcription factor with a molecular weight of ~35 kDa encoded by the ''PURA'' gene. It possesses ATP-independent dsDNA unwinding activity, and is known to bind sequence-specific purine-rich regions of ssDNA and ssRNA, recognizing GGN motifs. Purα is a member of the PUR family of proteins, which includes Purβ and two isoforms of Purγ. In its functional dimeric form Purα is known to repress expression of smooth muscle alpha actin (SMαA) encoded by the ''Acta2'' gene. It is also known to be involved in DNA replication and cell cycle regulation, as well as mRNA translation. It plays a crucial role in nervous system development, and has been implicated in two neurological diseases: PURA syndrome and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) (see Disease section).<ref>PMID:26744780</ref>
+[[Image:180503 PurA dimer.jpg|thumb|center|700px| Artist representation of a Purα homodimer (linkers between repeats I-II and III (red) were drawn in PowerPoint and are NOT to scale). NOTE: This is NOT a verified model, but a rough placement to show all three repeats together. It is not known what the orientation of these domains are relative to one another.  (Repeat I-II ([[5fgp]]): purple (I) and orange (II), repeat III ([[5fgo]]): cyan).]]
 == 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/2'>PUR repeat III</scene> facilitates dimerization through association with a repeat III from a second Purα monomer or repeat III of Purβ. Each PUR repeat is connected by flexible linker regions. 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.
+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 Purα they are not sequence-specific.
+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.
-The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues involved in protein-DNA conjugation are: <scene name='78/786627/Repeati_resi/2'>(repeat I) Q52, S53 and K54</scene>; <scene name='78/786627/Repeatii_resi/1'>(repeat II) K138, N140, R142, and F145</scene>. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 (repeat II) of the protein. This phenylalanine-guanine stacking interaction disrupts base-stacking within the DNA resulting in the following cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity.<ref>PMID:26744780</ref>
+The 2016 X-ray crystal structure of Purα repeat I-II ([[5fgp]]) shows DNA bound between repeats I and II. Residues indicated by this crystal structure to be involved in protein-DNA binding are: <scene name='78/786627/Repeati_resi/3'>(repeat I) Q52, S53 and K54</scene>; <scene name='78/786627/Repeatii_resi/1'>(repeat II) K138, N140, R142, and F145</scene>. K54 (repeat I) and K138 (repeat II) interact with the phosphate backbone, while Q52 (repeat I), S53 (repeat I), K54 (repeat I), R142 (repeat II), and N140 (repeat II) hydrogen bond directly with the DNA bases. Interestingly all bases appear to be stabilized by stacking interactions within the DNA strand except G4 which stacks directly with F145 in repeat II of the protein. This <scene name='78/786627/5fgp_57and145/3'>phenylalanine-guanine stacking interaction</scene> disrupts base-stacking within the DNA resulting in the neighboring cytosine being flipped out, introducing a strong kink in the DNA strand. This base-stacking interruption was shown to be responsible for Purα's DNA-unwinding activity by EMSA using a F145 mutant.<ref>PMID:26744780</ref>
 == Function ==
-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
+Purα binds to single stranded purine-rich regions of DNA or RNA. In particular, Purα (and Purβ) are known to bind the purine-rich tract containing an MCAT enhancer motif in the 5’ region of the sense strand of the smooth muscle alpha actin gene (''Acta2''). Purα functions as a repressor at both transcriptional and translational levels. At the level of transcription Purα (and Purβ) act in concert with Y-box-binding protein 1 (YB-1 in humans or MSY1 in mice) which binds the antisense pyrimidine-rich strand, together acting to repress ''Acta2'' expression. At the level of translation Purα, Purβ and MSY-1 (YB-1 in humans) have been shown to bind a region in exon 3 of ''Acta2'' mRNA that is structurally similar to the MCAT (AGGAATG) enhancer element and prevent transcription in fibroblasts.<ref>PMID:10608902</ref>
-<scene name='78/786627/5fgp_57and145/1'>Two aromatic residues</scene>, Y57 (repeat I) and F145 (repeat II) have been implicated in the DNA unwinding activity of PurA.<ref>PMID:26744780</ref>
+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.
 == 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 ==
 While Purα is a ubiquitously expressed protein in all cell types, it is generally found at low levels in most tissues. However, in adult humans and mice Purα expression is highest in the brain and spinal cord, and to a lesser extent in the testes. Purα has been shown to be upregulated in cardiac myocyte gap junctions following heart transplant in mice, colocalizing with SMαA.<ref>PMID:18344281</ref>
+== Interactions ==
+Purα is known to interact with:
+*Purβ
+*Serum response factor (SRF)
+*Sp1<ref>PMID:10457364</ref>
+*E2F-1<ref>PMID:10597240</ref>
+*Y-box-binding protein 1 (YB-1) (MSY1 in mice)<ref>PMID:10082537</ref>
+*Retinoblastoma protein (Rb)<ref>PMID:7592647</ref>
+*Rm62 RNA helicase (''Drosophila''), p68 RNA helicase (mammalian)<ref>PMID:21655086</ref>
+*JCV T-antigen<ref>PMID:8943069</ref>
+*Cyclin A/Cdk2 (PurA binds to the Cdk2 moiety)<ref>PMID:15707957</ref>
 == Disease ==
-Mutations in the ''PURA'' gene resulting in haploinsufficiency of Purα are known to cause the neurological disease PURA syndrome. PURA syndrome appears early in development, , with patients exhibiting severe developmental delay, seizures, feeding difficulty,  of severe intellectual disabilities, movements, vision,  hypotonia, premature telarche, . This disease has no cure, and life expectancy is .<ref>PMID:29097605</ref>. Purα knock-out mice exhibit similar neurological symptoms such as severe tremor developing at about postnatal week two, and feeding difficulties. These mice die after approximately one month. Heterozygous mice display less severe symptoms including seizures upon handling. <ref>PMID:25342064</ref>
+Mutations in the ''PURA'' gene resulting in haploinsufficiency are known to cause the neurological disease PURA syndrome, which has no cure. PURA syndrome appears early in development, with patients exhibiting severe developmental delay, seizures, feeding difficulty, intellectual disabilities, vision problems, hypotonia, and premature thelarche.<ref>PMID:29097605</ref> Purα knock-out mice exhibit similar neurological symptoms such as severe tremor developing at about postnatal week two, and feeding difficulties. These mice die after approximately one month. Heterozygous mice display less severe symptoms including seizures upon handling. <ref>PMID:25342064</ref> Interestingly, to date there have been no published accounts of phenotypic abnormalities in humans or mice with mutations in Purβ.
+Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is another disease associated with abnormal activity of Purα. In 2006, Johnson et al. observed that Purα colocalized with Fragile-X Mental Retardation Protein (FMRP) in mouse neuronal dendrites.<ref>PMID:16436378</ref> Purα also was found to be involved in dendritic mRNA transport, and in a ''Drosophila'' model of Fragile-X Tremor/Ataxia Syndrome it was hypothesized that the overexpression of ''FMR1'' mRNA (encoding FMRP) resulted in Purα being bound to these mRNAs leading to the apparent deficiency in Purα activity and accumulation of RNA-protein inclusion bodies resulting in FXTAS symptoms.<ref>PMID:17698009</ref><ref>PMID:21655086</ref>
+== The Storybook Version of Pur Protein History (Just for Fun!) ==
+In a lab across from central park in Manhattan, Edward Johnson and his postdoctoral fellow Andrew Bergemann stumbled on a protein in 1991 that would in years to come open doors to understanding diseases of neurological and cardiovascular origin. They named the protein Pur (pronounced “purr”) after its ability to bind a sequence of bent DNA rich in As and Gs, or purine nucleotides, called the “PUR element.” This region of DNA, found near the origin of replication, was thought to be involved in the regulation of DNA replication.<ref>PMID:1545807</ref> At the time, no sequence-specific single-stranded DNA binding proteins were known to exist. The novelty of the findings were tremendous, and paved the way for many future studies of sequence-specific DNA-binding proteins.
+While the focus of Johnson and Bergemann’s research was in DNA replication in cancer and AIDS, in the years that followed their discovery, Pur was found to interact with a tumor suppressor “retinoblastoma protein” or Rb. Likely as a result of funding available in cancer research and Rb, research has shifted from Pur’s role in DNA replication toward instead, its capacity to regulate transcription and translation, or the cellular processes involved in building proteins.
+In 1992, Bergemann, Johnson and Ma found what appeared to be a cousin of Pur. With only a C-terminal sequence to work from, the protein appeared to be similar but not identical to Pur. They named the putative protein “Purβ” and from then on referred to the original Pur protein as Purα.<ref>PMID:1448097</ref> Shortly thereafter in 1997, Kelm, et al. working to deduce the sequence of a protein they termed “vascular actin single-stranded DNA binding factor 2” (VACssBF2), isolated two different proteins of identical molecular weight to Purα and the putative Purβ. Upon sequencing and cloning of isolated cDNA, the team published the first full length sequence of what is now known to be Purβ.<ref>PMID:9334258</ref> Since this time, in humans three splice variants have been found of Purα, one of Purβ and two isoforms of another Pur family member Purγ: Purγ-A and Purγ-B.
+Purγ has been studied to a far lesser degree than Purα and Purβ. While little is yet known about the actions of the Purγ protein, Johnson and Liu in 2002 found that the Purγ-A isoform mRNA was expressed at very low levels or not at all in normal human tissues, but highly expressed in a panel of cancer cell types.<ref>PMID:12034829</ref> Similarly, Purγ-B mRNA was absent in human tissues except the testes, and in several tumor tissue types. Most of the research surrounding the Pur family of proteins has focused on Purα due to its involvement in neurological disorders, however interest in Purβ has increased in recent years as it has been implicated in cardiovascular disease, fibrosis and acute myelogenous leukemia.<ref>PMID:27064749</ref>
+== 3D Structures of Purα ==
+*[[5fgp]] (I-II repeat complex with DNA. ''Drosophila m.'')<ref>PMID:19846792</ref>
+*[[5fgo]] (III repeat dimer. ''Drosophila m.'')<ref>PMID:26744780</ref>
+*[[3k44]] (I-II repeat, apo. ''Drosophila m.'')<ref>PMID:26744780</ref>
+*[[3nm7]] (Apo. ''Borrelia b.'' Note: the ''Borrelia'' homolog of Purα contains only one PUR repeat)<ref>PMID:20976240</ref>
+*[[3n8b]] (Apo. ''Borrelia b.'' Note: the ''Borrelia'' homolog of Purα contains only one PUR repeat)<ref>PMID:20976240</ref>
-Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is another disease associated with abnormal activity of Purα. Normally between __ and __ copies of __ , however in greater than __ copies can result in ___ causing delayed-onset neurological problems. FXTAS generally develops in middle age, and is characterized by tremor, ataxia, and ___.
+== Additional Resources ==
+For more information on PURA syndrome, visit the PURA Syndrome Foundation website: [https://www.purasyndrome.org]
-JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>
+This page was created using JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref>
 == References ==
 <references/>