1t6j

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[[Image:1t6j.gif|left|200px]]
 
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==Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides==
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The line below this paragraph, containing "STRUCTURE_1t6j", creates the "Structure Box" on the page.
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<StructureSection load='1t6j' size='340' side='right'caption='[[1t6j]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1t6j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T6J FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=175:3,5-DIHYDRO-5-METHYLIDENE-4H-IMIDAZOL-4-ON'>175</scene>, <scene name='pdbligand=CIN:4-CARBOXYCINNAMIC+ACID'>CIN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_1t6j| PDB=1t6j | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1t6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t6j OCA], [https://pdbe.org/1t6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t6j RCSB], [https://www.ebi.ac.uk/pdbsum/1t6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t6j ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t6/1t6j_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1t6j ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The first three-dimensional structure of phenylalanine ammonia lyase (PAL) has been determined at 2.1 A resolution for PAL from Rhodosporidium toruloides. The enzyme is structurally similar to the mechanistically related histidine ammonia lyase (HAL), with PAL having an additional approximately 160 residues extending from the common fold. We propose that catalysis (including lowering the pK(a) of nonacidic C3 of l-phenylalanine for an E1cb mechanism) is potentially governed by dipole moments of seven alpha helices associated with the PAL active site (six positive poles and one negative pole). Cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. The helix dipoles appear fully compatible with a model of phenylalanine docked in the active site of PAL having the first covalent bond formed between the amino group of substrate and the methylidene group of MIO: 12 highly conserved residues (near the N termini of helices for enhancing function) are poised to serve roles in substrate recognition, MIO activation, product separation, proton donation, or polarizing electrons from the phenyl ring of substrate for activation of C3; and a highly conserved His residue (near the C terminus of the one helix that directs its negative pole toward the active site to increase the residue's basicity) is positioned to act as a general base, abstracting the pro-S hydrogen from C3 of substrate. A similar mechanism is proposed for HAL, which has a similar disposition of seven alpha helices and similar active-site residues. The helix dipoles appear incompatible with a proposed mechanism that invokes a carbocation intermediate.
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'''Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides'''
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Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis.,Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T Biochemistry. 2004 Sep 14;43(36):11403-16. PMID:15350127<ref>PMID:15350127</ref>
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==Overview==
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The first three-dimensional structure of phenylalanine ammonia lyase (PAL) has been determined at 2.1 A resolution for PAL from Rhodosporidium toruloides. The enzyme is structurally similar to the mechanistically related histidine ammonia lyase (HAL), with PAL having an additional approximately 160 residues extending from the common fold. We propose that catalysis (including lowering the pK(a) of nonacidic C3 of l-phenylalanine for an E1cb mechanism) is potentially governed by dipole moments of seven alpha helices associated with the PAL active site (six positive poles and one negative pole). Cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) resides atop the positive poles of three helices, for increasing its electrophilicity. The helix dipoles appear fully compatible with a model of phenylalanine docked in the active site of PAL having the first covalent bond formed between the amino group of substrate and the methylidene group of MIO: 12 highly conserved residues (near the N termini of helices for enhancing function) are poised to serve roles in substrate recognition, MIO activation, product separation, proton donation, or polarizing electrons from the phenyl ring of substrate for activation of C3; and a highly conserved His residue (near the C terminus of the one helix that directs its negative pole toward the active site to increase the residue's basicity) is positioned to act as a general base, abstracting the pro-S hydrogen from C3 of substrate. A similar mechanism is proposed for HAL, which has a similar disposition of seven alpha helices and similar active-site residues. The helix dipoles appear incompatible with a proposed mechanism that invokes a carbocation intermediate.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1T6J is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T6J OCA].
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</div>
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<div class="pdbe-citations 1t6j" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis., Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T, Biochemistry. 2004 Sep 14;43(36):11403-16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15350127 15350127]
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*[[Aminomutase 3D structures|Aminomutase 3D structures]]
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[[Category: Phenylalanine ammonia-lyase]]
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== References ==
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[[Category: Rhodosporidium toruloides]]
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<references/>
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[[Category: Single protein]]
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__TOC__
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[[Category: Calabrese, J C.]]
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</StructureSection>
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[[Category: Jordan, D B.]]
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[[Category: Large Structures]]
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[[Category: Cinnamate]]
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[[Category: Rhodotorula toruloides]]
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[[Category: Mio]]
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[[Category: Calabrese JC]]
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[[Category: Triple helix coiled coil]]
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[[Category: Jordan DB]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:35:33 2008''
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Current revision

Crystal Structure of Phenylalanine Ammonia Lyase from Rhodosporidium toruloides

PDB ID 1t6j

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