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Pancreatic and Duodenal homeoboX 1, called PDX-1, is a transcription factor which is encoded by the gene ''Ipf1''. This one is located at the human chromosome 13q12.1.
Pancreatic and Duodenal homeoboX 1, called PDX-1, is a transcription factor which is encoded by the gene ''Ipf1''. This one is located at the human chromosome 13q12.1.




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Human PDX-1 is a protein of 283 amino acids with a molecular weight of 30,64 kDa. This transcription factor belongs to the ParaHox transcription factor family, which diverged from the Hox subfamily through a duplication event.
Human PDX-1 is a protein of 283 amino acids with a molecular weight of 30,64 kDa. This transcription factor belongs to the ParaHox transcription factor family, which diverged from the Hox subfamily through a duplication event.
Moreover, it is important to note that PDX-1 is located in the nucleus of cells.  
Moreover, it is important to note that PDX-1 is located in the nucleus of cells.  




[[Image:Schematic representation of functional domains and phosphorylation sites of PDX-1.jpg|right|580px|thumb|'''Schematic representation of functional domains and phosphorylation sites of PDX-1''']]
[[Image:Schematic representation of functional domains and phosphorylation sites of PDX-1.jpg|right|580px|thumb|'''Schematic representation of functional domains and phosphorylation sites of PDX-1''']]


PDX-1 contains, at the N-terminus, a transactivation domain ( from 1 to 79 amino acids) and the middle region of the protein is composed of a homeodomain (from 146 to 206 amino acids) which is essential for DNA binding and protein-protein interactions.
PDX-1 contains, at the N-terminus, a transactivation domain (from 1 to 79 amino acids) and the middle region of the protein is composed of a homeodomain (from 146 to 206 amino acids) which is essential for DNA binding and protein-protein interactions.




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<ref> PMID: 17315980 </ref> <ref name = "binding" >PMID: 23950697</ref>  
<ref> PMID: 17315980 </ref> <ref name = "binding" >PMID: 23950697</ref>  
[[Image:Pdx1.jpg|left|200px|thumb|'''General structure of PDX-1 homeodomain''']]
[[Image:Pdx1.jpg|left|230px|thumb|'''General structure of PDX-1 homeodomain''']]


===='''Generality''' ====
===='''Generality''' ====
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The homeodomain is one of several small DNA binding motifs with DNA binding specificity which is present into approximately 235 transcription factors.
The homeodomain is one of several small DNA binding motifs with DNA binding specificity which is present into approximately 235 transcription factors.
The homeodomain protein folds into three α-helices ([http://en.wikipedia.org/wiki/Alpha_helix Wikipédia]), with helices 1 and 2 antiparallel to each other and perpendicular to helix 3, and a flexible N-terminal arm.  
The homeodomain protein folds into three <scene name='56/568027/Helices/1'>three α-helices</scene> ([http://en.wikipedia.org/wiki/Alpha_helix Wikipédia]), with helices 1 and 2 antiparallel to each other and perpendicular to helix 3, and a flexible <scene name='56/568027/Nterminal/1'>N-terminal arm</scene>.  


Helices 2 and 3 form a helix-turn-helix type motif. ([http://proteopedia.org/wiki/index.php/Helix-turn-helix_motif  Protéopédia], [http://en.wikipedia.org/wiki/Helix-turn-helix Wikipedia])
Helices 2 and 3 form a helix-turn-helix type motif ([http://proteopedia.org/wiki/index.php/Helix-turn-helix_motif  Protéopédia], [http://en.wikipedia.org/wiki/Helix-turn-helix Wikipedia]).
Indeed this tertiary structure motif consists of two α-helices and a short extended amino acids chain between them. The more carboxyl-terminal helix can fit into the major groove of DNA.   
Indeed this tertiary structure motif consists of two α-helices and a short extended amino acids chain between them. The more carboxyl-terminal helix can fit into the major groove of DNA.   
That is why, helix 3 (also known as the recognition helix) interacts with the the major groove of the DNA.  
That is why, helix 3 (also known as the recognition helix) interacts with the the major groove of the DNA.  
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===='''Motifs of the PDX-1 homeodomain''' [http://www.proteopedia.org/wiki/index.php/Image:Schematic_representation_of_functional_domains_and_phosphorylation_sites_of_PDX-1.jpg] ====   
===='''Motifs of the PDX-1 homeodomain''' [[http://www.proteopedia.org/wiki/index.php/Image:Schematic_representation_of_functional_domains_and_phosphorylation_sites_of_PDX-1.jpg]] ====   


The homeodomain contains a Protein Transduction Domain (PTD : from 188 to 203 amino acids) and a Nuclear Localization Signal motif (NLS : from 197 to 203 amino acids), which allow PDX-1 to permeate into cells.  
The homeodomain contains a Protein Transduction Domain (PTD : from 188 to 203 amino acids) and a Nuclear Localization Signal motif (NLS : from 197 to 203 amino acids), which allow PDX-1 to permeate into cells.  
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Nuclear translocation of transcription factors is a crucial requirement for their action and stimulus-dependent nuclear translocation can serve as a mechanism to regulate gene expression at the level of transcription initiation.
Nuclear translocation of transcription factors is a crucial requirement for their action and stimulus-dependent nuclear translocation can serve as a mechanism to regulate gene expression at the level of transcription initiation.
NLS is composed of several basic amino acids such as arginine (R) and lysine (K), as we can see in the NLS sequence RRMKWKK (basic amino acids) of PDX-1. This motif is sufficient for the nuclear import of PDX-1.<ref>PMID : 10567702</ref>  
NLS is composed of several basic amino acids such as arginine (R) and lysine (K), as we can see in the NLS sequence RRMKWKK (basic amino acids) of PDX-1. This motif is sufficient for the nuclear import of PDX-1.<ref>PMID : 10567702</ref>  




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All recognition helices (also, called helices 3) of Hox factors (such as PDX-1) are able to recognize the TAAT core of the DNA through van der Waals contacts made by Ile 47 with Ade 3 and Thy 4, and through two hydrogen bonds by Asn 51 with Ade 3. Asn 51 also forms a hydrogen bond with Ade 2. Finally, bases Cyt 5*, Thy 6*, and Cyt 7* are recognized through van der Waals contacts with Gln 50 and Met 54. [[http://www.proteopedia.org/wiki/index.php/Image:Nter.jpg ] '''Part B''']   
All recognition helices (also, called helices 3) of Hox factors (such as PDX-1) are able to recognize the TAAT core of the DNA through van der Waals contacts made by Ile 47 with Ade 3 and Thy 4, and through two hydrogen bonds by <scene name='56/568027/Asn51/1'>Asn 51</scene> with Ade 3. Asn 51 also forms a hydrogen bond with Ade 2. Finally, bases Cyt 5*, Thy 6*, and Cyt 7* are recognized through van der Waals contacts with Gln 50 and Met 54. [[http://www.proteopedia.org/wiki/index.php/Image:Nter.jpg ] '''Part B''']   


The N-terminal arm sequence is less well conserved than the recognition helix, but typically includes positively charged Lys or Arg residues. The arm sequence contributes to DNA binding specificity. The N-terminal arm facilitates searching the DNA for binding sites through electro-static attraction by a sliding mechanism or transferring between DNA strands by a ‘‘fly catching’’ mechanism.
The N-terminal arm sequence is less well conserved than the recognition helix, but typically includes positively charged <scene name='56/568027/Lysarg/1'>Lys or Arg residues</scene>. The arm sequence contributes to DNA binding specificity. The N-terminal arm facilitates searching the DNA for binding sites through electro-static attraction by a sliding mechanism or transferring between DNA strands by a ‘‘fly catching’’ mechanism.




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Majors differences between conformations A and B  are in the major groove. Three phosphate contacts are specific to conformation A: Asn 51 with Ade 2, and Arg 31 and Lys 46 with Ade 8*. However, conformation B is more specific than conformation A.  
Majors differences between conformations A and B  are in the major groove. Three phosphate contacts are specific to conformation A: Asn 51 with Ade 2, and Arg 31 and Lys 46 with Ade 8*. However, conformation B is more specific than conformation A.  


Actually, in conformation B, Gln 50 formes a water-mediated contact with Gua 5 and Thy 6* , and Asn 51 binds Ade 2 in addition to Ade 3.  
Actually, in conformation B, Gln 50 formes a water-mediated contact with Gua 5 and Thy 6* , and <scene name='56/568027/Asn51/1'>Asn 51</scene> binds Ade 2 in addition to Ade 3.  




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''* The N-terminal arm ''
The <scene name='56/568027/Nterminal/1'>N-terminal arm</scene> (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains <scene name='56/568027/Basicresidues/2'>three basic residues</scene> :  Lys 2, Arg 3 and Arg 5.
In both PDX-1 conformations, Arg 5 forms hydrogen bonds with the bases of Thy 1 and Gua -1* through the minor groove, and van der Waals contact with Ade 2.
In conformation B, the N-terminal arm is more ordered with Lys 2 hydrogen bonded with the bases Ade 3 and Thy 2* in the minor groove, whereas in the conformation A, the N-terminal arm is mostly disordered. Scientists attributed the different contacts between the two conformations, to differences in DNA bending.
Arg 3 and Arg 43  help the stabilization of the N-terminal arm. In fact, the contact by <scene name='56/568027/Arg/1'>Arg 3 and Arg 43</scene> from the major groove with the phosphate backbone correlates with stabilizing the N-terminal arm. Moreover, these residues are more mobile in conformation A than in conformation B.
So, the most stable  configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43.




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''* The N-terminal arm ''




The N-terminal arm  (residues 1 to 9) of PDX-1 homeodomain, first contacts the core TAAT bases of the DNA through the minor groove and contributes to the binding specificity. In PDX-1, the N-terminal sequence contains three basic residues :  Lys 2, Arg 3 and Arg 5.
In both PDX-1 conformations, Arg 5 forms hydrogen bonds with the bases of Thy 1 and Gua -1* through the minor groove, and van der Waals contact with Ade 2.


In conformation B, the N-terminal arm is more ordered with Lys 2 hydrogen bonded with the bases Ade 3 and Thy 2* in the minor groove, whereas in the conformation A, the N-terminal arm is mostly disordered. Scientists attributed the different contacts between the two conformations, to differences in DNA bending.


Arg 3 and Arg 43  help the stabilization of the N-terminal arm. In fact, the contact by Arg 3 and Arg 43 from the major groove with the phosphate backbone correlates with stabilizing the N-terminal arm. Moreover, these residues are more mobile in conformation A than in conformation B.


So, the most stable  configuration for the N-terminal arm of Pdx1 consists of Lys 2 inserted in the minor groove and Arg 3 outside of the minor grove contacting the phosphate backbone and Arg 43.




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In order to regulate all of these genes, PDX1 interacts with different cofactors.  
In order to regulate all of these genes, PDX1 interacts with different cofactors.  


In pancreatic δ-cells, PDX-1 interacts with PBX1 and PREP1 corresponding respectively to PBC and MEIS proteins. These proteins belong to the three amino acids loop extension (TALE) family of homeodomains. By interacting with these proteins, PDX-1 can regulate the somatostatin promoter. Interaction with the TALE proteins is mediated through a conserved pentapeptide motif, FPWMK, located at the 10 residues of the N-terminal of the homeodomain. <ref>PMID : 11279116</ref>  
In pancreatic δ-cells, PDX-1 interacts with PBX1 and PREP1 corresponding respectively to PBC and MEIS proteins. These proteins belong to the three amino acids loop extension (TALE) family of homeodomains. By interacting with these proteins, PDX-1 can regulate the somatostatin promoter. Interaction with the TALE proteins is mediated through a conserved pentapeptide motif, FPWMK, located in the N-terminal region of the protein and separated from the homeodomain by around 10 residues. <ref>PMID : 11279116</ref>  


In neural cells, PDX-1 utilizes a different binding site on the somatostatin promoter than in δ-cells, suggesting a distinct protein complex. PDX-1 interacts also with the basic helix-loop-helix (bHLH: [http://en.wikipedia.org/wiki/Basic_helix-loop-helix Wikipedia]) factor E47/NeuroD.  
In neural cells, PDX-1 utilizes a different binding site on the somatostatin promoter than in δ-cells, suggesting a distinct protein complex. PDX-1 interacts also with the basic helix-loop-helix (bHLH: [http://en.wikipedia.org/wiki/Basic_helix-loop-helix Wikipedia]) factor E47/NeuroD.  
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