2zy4
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 2zy4 is ON HOLD Authors: Chen, H.-J., Ko, T.-P., Lee, C.-Y., Wang, N.-C., Wang, A.H.-J. Description: dodecameric L-aspartate beta-decarboxylase ''...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==dodecameric L-aspartate beta-decarboxylase== | |
| + | <StructureSection load='2zy4' size='340' side='right'caption='[[2zy4]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[2zy4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis_subsp._faecalis Alcaligenes faecalis subsp. faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZY4 FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zy4 OCA], [https://pdbe.org/2zy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zy4 RCSB], [https://www.ebi.ac.uk/pdbsum/2zy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zy4 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/ASDA_COMTE ASDA_COMTE] Bifunctional enzyme that has both L-aspartate decarboxylase and transaminase activity.<ref>PMID:19368885</ref> [PDB:2ZY3] | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zy/2zy4_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=2zy4 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The type-I PLP enzyme l-aspartate beta-decarboxylase converts aspartate to alanine and CO(2). Similar to the homodimeric aminotransferases, its protein subunit comprises a large and a small domain, of 410 and 120 residues, respectively. The crystal structure reveals a dodecamer made of six identical dimers arranged in a truncated tetrahedron whose assembly involves tetramer and hexamer as intermediates. The additional helical motifs I and II participate in the oligomer formation. Triple mutations of S67R/Y68R/M69R or S67E/Y68E/M69E in motif I produced an inactive dimer. The PLP is bound covalently to Lys315 in the active site, while its phosphate group interacts with a neighboring Tyr134. Removal of the bulky side chain of Arg37, which overhangs the PLP group, improved the substrate affinity. Mutations in flexible regions produced the more active K17A and the completely inactive R487A. The structure also suggests that substrate binding triggers conformational changes essential for catalyzing the reaction. | ||
| - | + | Structure, assembly, and mechanism of a PLP-dependent dodecameric L-aspartate beta-decarboxylase.,Chen HJ, Ko TP, Lee CY, Wang NC, Wang AH Structure. 2009 Apr 15;17(4):517-29. PMID:19368885<ref>PMID:19368885</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 2zy4" style="background-color:#fffaf0;"></div> | ||
| - | + | ==See Also== | |
| + | *[[Aspartate decarboxylase 3D structures|Aspartate decarboxylase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Alcaligenes faecalis subsp. faecalis]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Chen H-J]] | ||
| + | [[Category: Ko T-P]] | ||
| + | [[Category: Lee C-Y]] | ||
| + | [[Category: Wang AH-J]] | ||
| + | [[Category: Wang N-C]] | ||
Current revision
dodecameric L-aspartate beta-decarboxylase
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