Sandbox Reserved 770: Difference between revisions
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'''pH Dependence''': Optimal pH=8.5 <ref name="geninfo">http://www.uniprot.org/uniprot/P11544</ref> | '''pH Dependence''': Optimal pH=8.5 <ref name="geninfo">http://www.uniprot.org/uniprot/P11544</ref> | ||
==Secondary Structure== | ==Subunits Description (Secondary Structure) and Quaternary Structure== | ||
[[Image:Seahorse.png|thumb|left|Figure 2. Subunit B (colored red) of PAL tetramer in both ribbon and surface representations. Cinnamic acid, a product formed from by L-Phe catalysis, is also shown in this figure. <ref name=rutgers>http://maptest.rutgers.edu/drupal/?q=node/408</ref>.]] | [[Image:Seahorse.png|thumb|left|Figure 2. Subunit B (colored red) of PAL tetramer in both ribbon and surface representations. Cinnamic acid, a product formed from by L-Phe catalysis, is also shown in this figure. <ref name=rutgers>http://maptest.rutgers.edu/drupal/?q=node/408</ref>.]] | ||
[[Image:Quaternary_Structure.gif|thumb|right|Figure 3. Quaternary Structure of PAL. The four individual monomers are color-coded in red, green, blue, and yellow, displaying the approximate 222 symmetry of the PAL tetramer.(a) Stereoview of PAL from a side perspective. The bracketed areas represent the residues, arranged in a fan, that are present in PAL and absent in HAL. (b) Top perspective of the PAL tetramer. This view looks down into the active sites of two of the subunits; the other two active sites would be seen from a bottom view.]] | [[Image:Quaternary_Structure.gif|thumb|right|Figure 3. Quaternary Structure of PAL. The four individual monomers are color-coded in red, green, blue, and yellow, displaying the approximate 222 symmetry of the PAL tetramer.(a) Stereoview of PAL from a side perspective. The bracketed areas represent the residues, arranged in a fan, that are present in PAL and absent in HAL. (b) Top perspective of the PAL tetramer. This view looks down into the active sites of two of the subunits; the other two active sites would be seen from a bottom view.]] | ||
Phenylalanine ammonia lyase enzyme is a dimer composed of two identical subunits. <ref name="crystallization">http://ci.nii.ac.jp/els/110006324658.pdf?id=ART0008332067&type=pdf&lang=en&host=cinii&order_no=&ppv_type=0&lang_sw=&no=1386328093&cp=</ref> Each subunit of PAL from ''R. toruloides'' assume a "seahorse" shape by interlocking head-to-tail, creating overlapping regions with two adjacent subunits, as shown by Figure 2. These overlapping regions maximize interactions between subunits, giving rise to the formation of the tightly assembled tetramer, as shown in Figure 3. Formation of the tetramer buries 58% of their combined surfaces. <ref name=crystal>http://pubs.acs.org.prox.lib.ncsu.edu/doi/pdfplus/10.1021/bi049053%2B</ref> Of the 66 interactions between adjacent subunits, 25 hydrogen bonding interactions exists between Asp & Glu carboxylate oxygens and NH2 & OH moieties, including a prominent band of Asp & Glu interactions with Arg side chains between subunits nearby the central bundle of helices. PAL's central core is comprised of parallel alpha helices of varying lengths. There is only one section of Beta sheet longer than three residues in PAL, which resides in the funnel region leading to the active site. PAL and HAL (Histadine Ammonia Lyase) contain similar folds, but PAL differs from HAL with 215 additional residues. Of the 215 residues from this section, 155 residues extend above and below the main body of the structure, creating a "fan" arrangement, shown as the bracketed areas in Figure 3a. | Phenylalanine ammonia lyase enzyme is a dimer composed of two identical subunits. <ref name="crystallization">http://ci.nii.ac.jp/els/110006324658.pdf?id=ART0008332067&type=pdf&lang=en&host=cinii&order_no=&ppv_type=0&lang_sw=&no=1386328093&cp=</ref> Each subunit of PAL from ''R. toruloides'' assume a "seahorse" shape by interlocking head-to-tail, creating overlapping regions with two adjacent subunits, as shown by Figure 2. These overlapping regions maximize interactions between subunits, giving rise to the formation of the tightly assembled tetramer, as shown in Figure 3. Formation of the tetramer buries 58% of their combined surfaces. <ref name=crystal>http://pubs.acs.org.prox.lib.ncsu.edu/doi/pdfplus/10.1021/bi049053%2B</ref> Of the 66 interactions between adjacent subunits, 25 hydrogen bonding interactions exists between Asp & Glu carboxylate oxygens and NH2 & OH moieties, including a prominent band of Asp & Glu interactions with Arg side chains between subunits nearby the central bundle of helices. PAL's central core is comprised of parallel alpha helices of varying lengths. There is only one section of Beta sheet longer than three residues in PAL, which resides in the funnel region leading to the active site. PAL and HAL (Histadine Ammonia Lyase) contain similar folds, but PAL differs from HAL with 215 additional residues. Of the 215 residues from this section, 155 residues extend above and below the main body of the structure, creating a "fan" arrangement, shown as the bracketed areas in Figure 3a. | ||
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[[Image:Positive_Negative_Helices_PAL.png|thumb|left|Figure 6. Six positive poles toward the active site, one negative pole toward the active site]] | [[Image:Positive_Negative_Helices_PAL.png|thumb|left|Figure 6. Six positive poles toward the active site, one negative pole toward the active site]] | ||
