1y2m

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[[Image:1y2m.png|left|200px]]
 
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==Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides==
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The line below this paragraph, containing "STRUCTURE_1y2m", creates the "Structure Box" on the page.
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<StructureSection load='1y2m' size='340' side='right'caption='[[1y2m]], [[Resolution|resolution]] 1.60&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'>[[1y2m]] is a 4 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=1Y2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y2M 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]] 1.6&#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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_1y2m| PDB=1y2m | 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=1y2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y2m OCA], [https://pdbe.org/1y2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y2m RCSB], [https://www.ebi.ac.uk/pdbsum/1y2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y2m 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/y2/1y2m_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=1y2m 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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Structure-based protein engineering coupled with chemical modifications (e.g., pegylation) is a powerful combination to significantly improve the development of proteins as therapeutic agents. As a test case, phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) was selected for enzyme replacement therapy in phenylketonuria [C.R. Scriver, S. Kaufman, Hyperphenylalaninemia:phenylalanine Hydroxylase Deficiency. The Metabolic and Molecular Bases of Inherited Disease, McGraw-Hill, New York, 2001, Chapter 77], an inherited metabolic disorder (OMIM 261600) causing mental retardation due to deficiency of the enzyme l-phenylalanine hydroxylase (EC 1.14.16.1). Previous in vivo studies of recombinant PAL demonstrated a lowering of blood l-phenylalanine levels; yet, the metabolic effect was not sustained due to protein degradation and immunogenicity [C.N. Sarkissian, Z. Shao, F. Blain, R. Peevers, H. Su, R. Heft, T.M. Chang, C.R. Scriver, A different approach to treatment of phenylketonuria:phenylalanine degradation with recombinant phenylalanine ammonia lyase, Proc. Natl. Acad. Sci. USA 96 (1999) 2339; J.A. Hoskins, G. Jack, H.E. Wade, R.J. Peiris, E.C. Wright, D.J. Starr, J. Stern, Enzymatic control of phenylalanine intake in phenylketonuria, Lancet 1 (1980) 392; C.M. Ambrus, S. Anthone, C. Horvath, K. Kalghatgi, A.S. Lele, G. Eapen, J.L. Ambrus, A.J. Ryan, P. Li, Extracorporeal enzyme reactors for depletion of phenylalanine in phenylketonuria, Ann. Intern. Med. 106 (1987) 531]. Here, we report the 1.6A three-dimensional structure of Rhodosporidium toruloides PAL, structure-based molecular engineering, pegylation of PAL, as well as in vitro and in vivo PKU mouse model studies on pegylated PAL formulations. Our results show that pegylation of R. toruloides PAL leads to promising therapeutic efficacy after subcutaneous injection by enhancing the in vivo activity, lowering plasma phenylalanine, and leading to reduced immunogenicity. The three-dimensional structure of PAL provides a basis for understanding the properties of pegylated forms of PAL and strategies for structure-based re-engineering of PAL for PKU treatment.
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===Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides===
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Structure-based chemical modification strategy for enzyme replacement treatment of phenylketonuria.,Wang L, Gamez A, Sarkissian CN, Straub M, Patch MG, Han GW, Striepeke S, Fitzpatrick P, Scriver CR, Stevens RC Mol Genet Metab. 2005 Sep-Oct;86(1-2):134-40. Epub 2005 Jul 11. PMID:16006165<ref>PMID:16006165</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1y2m" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16006165}}, adds the Publication Abstract to the page
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*[[Aminomutase 3D structures|Aminomutase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16006165 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16006165}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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[[1y2m]] is a 4 chain structure with 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=1Y2M OCA].
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[[Category: Rhodotorula toruloides]]
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[[Category: Gamez A]]
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==Reference==
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[[Category: Han GW]]
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<ref group="xtra">PMID:16006165</ref><ref group="xtra">PMID:10051643</ref><references group="xtra"/>
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[[Category: Patch MG]]
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[[Category: Lyase]]
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[[Category: Sarkissian CN]]
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[[Category: Rhodosporidium toruloides]]
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[[Category: Scriver CR]]
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[[Category: Gamez, A.]]
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[[Category: Stevens RC]]
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[[Category: Han, G W.]]
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[[Category: Straub M]]
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[[Category: Patch, M G.]]
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[[Category: Wang L]]
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[[Category: Sarkissian, C N.]]
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[[Category: Scriver, C R.]]
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[[Category: Stevens, R C.]]
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[[Category: Straub, M.]]
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[[Category: Wang, L.]]
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[[Category: Alpha helice]]
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[[Category: Lyase]]
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Current revision

Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides

PDB ID 1y2m

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