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| '''p300/CBP-associated factor''' (PCAF), <ref> sample ref </ref> | | '''p300/CBP-associated factor''' (PCAF), <ref> sample ref </ref> |
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| == '''Structure''' == | | == '''Structure and Function''' == |
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| Structure stuff<ref> sample ref </ref>
| | The bromodomain was originally identified as a sequence of roughly 60 amino acid residues that forms 2 alpha helices. Haynes, S.R. et al (1992) Nucleic Acids Res. 20, 2603. However, it is now known that the bromodomain consist of a highly conserved sequence of approximately 110 amino acids. Owen, D. J. et al. (2000) EMBO J. 19(22), 6141. The structure of the PCAF bromodomain consists of a four-helix bundle (alphaZ, aA,aB, and aC) with a left-handed twist, and a long intervening loop between helices Z and A (ZA loop). Dhalluin. The ZA loop of the bromodomain has a defined conformation and is packed against the loop between helices aB and aC (BC loop) to form a hydrophobic pocket. This pocket created by the ZA and BC loops is lined by specific residues (Val 752, Ala 757, Tyr 760, Val 763, Tyr 802 and Tyr 809) that support protein-protein interactions. The ZA loop varies in length between different bromodomains, but almost always contains residues corresponding to Phe 748, Pro 751, Pro 758, Tyr 760 and Pro 767. Dhalluin. |
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| '''Catalytic Domain'''
| | The hydrophobic pocket formed by the loops is the primary binding site for acetyl-lysine proteins. This interaction has been shown via localization and chemical shift experiments that revealed the specific manner with which the bromodomain hydrophobic cavity binds to acetylated lysine residues. Once the acetyl-lysine residue makes the initial binding inside the hydrophobic pocket, the ZA and BC loop residues at the entrance of the pocket interact with the amino acids adjacent (+/- 1 or 2) to the already bound acetyl-lysine. Those interactions reinforce binding of the target sequence. Mujtaba, S. et al (2007) Oncogene 26, 5521. Small structural changes in the conformation of the ZA and BC loops result in exposing other residues that are originally buried within the protein to aid in peptide recognition. Mujtaba, S. et al (2002) Mol. Cell 9, 575. |
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| The <scene name='Sandbox_Reserved_642/Catalytic_domain/1'>catalytic domain</scene> of phenylalanine hydroxylase includes resides 143-410. This region has a basket-like arrangement consisting of 13 alpha-helices and 8 beta-strands. This region of the protein also includes the active site. The active site of PheOH can be found in the center of the catalytic domain and is characterized by a 13 Angstroms deep and 10 Angstroms wide hydrophobic pocket. Lining the active site are 3 glutamates, 2 histadines and 1 tyrosine residue along with hydrophobic residues for a total of 34 amino acids. Covering the entrance of the active site is a short loop consisting or residues 378-381. | |
| The center of each catalytic domain consists of an iron ion which is vital to the enzyme activity. The iron atom binds in the active site to <scene name='Sandbox_Reserved_642/Iron_binding/2'>histadine residues 285 and 290, 1 oxygen atom in glutamate 330</scene>. Histadine 285 and 290 were found to be required for the binding of iron through site directed mutagenisis studies. The iron ions are coordinated to three water molecules and arrange in an octahedral geometry. The active site also binds the
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| <scene name='Sandbox_Reserved_642/Cofactor/1'>cofactor tetrahydrobiopterin</scene>. This cofactor binds closely to the iron ion and forms hydrogen bonds with two of the three water molecules. The cofactor also forms hydrogen bonds with the carbonyl oxygen of the protein residues including Ala322, Gly247, and Leu249 and the amide of Leu249.<ref> Erlandsen H., DirSci; Marianne G. Patch, PhD; Alejandra Gamez, PhD; Mary Straub; and Raymond C. Stevens, PhD. Structural Studies on Phenylalanine Hydroxylase and Implications Toward Understanding and Treating Phenylketonuria [http://www.pkuworld.org/home/docs/literature/erlandsen_2003_p.pdf]</ref>
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| '''Tetramerization Domain'''
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| Phenylalanine Hydroxylase exists in equilibrium between a homodimer and a homotetramer. The region responsible for the tertamerization is the <scene name='Sandbox_Reserved_642/Tetramerization_domain/1'>tetramerization domain</scene> located at the C terminal end of the protein. It consists of residues 411-452. The tetramerization domain consists of 2 beta-strands forming a beta-ribbon and an alpha-helix that is 40 angstroms long. The four alpha helices, consisting of one from each monomer, pack into a coil coil motif with the helices arranged in an anti-parallel manner.<ref> Erlandsen H., DirSci; Marianne G. Patch, PhD; Alejandra Gamez, PhD; Mary Straub; and Raymond C. Stevens, PhD. Structural Studies on Phenylalanine Hydroxylase and Implications Toward Understanding and Treating Phenylketonuria [http://www.pkuworld.org/home/docs/literature/erlandsen_2003_p.pdf]</ref>
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| '''Regulatory Domain'''
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| Housed in the N-terminus, the regulatory domain contains residues 19-142 and is more flexible than the other domains. The core of this domain contains an alpha beta sandwich and a beta alpha beta double motif. <ref> Bostjan Kobe, Ian G. Jennings, Colin M. House1, Belinda J. Michell, Kenneth E. Goodwill, Bernard D. Santarsiero, Raymond C. Stevens, Richard G. H. Cotton and Bruce E. Kemp. Nature Structural Biology 6, 442 - 448 (1999), Structural basis of autoregulation of phenylalanine hydroxylase, [http://http://www.nature.com/nsmb/journal/v6/n5/full/nsb0599_442.html]</ref>
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| == '''Mechanism''' == | | == '''Mechanism''' == |
