Vanessa Chaplin/sandbox2: Difference between revisions
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Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref> | Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref> | ||
These HIF-hydroxylase enzymes include Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref> | These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate the Pro-564 position. | ||
Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (PHD2)]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to gaining further knowledge of oxygen sensing. | |||
<structure load='2g19' size='335' frame='true' align='right' | <structure load='2g19' size='335' frame='true' align='right' | ||
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' /> | caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' /> | ||
<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene> | <scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene> | ||