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1dqx

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[[Image:1dqx.jpg|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==
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|PDB= 1dqx |SIZE=350|CAPTION= <scene name='initialview01'>1dqx</scene>, resolution 2.40&Aring;
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<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=BMP:6-HYDROXYURIDINE-5&#39;-PHOSPHATE'>BMP</scene>
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<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23]
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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]] 2.4&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>
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}}
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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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [https://pdbe.org/1dqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [https://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PYRF_YEAST PYRF_YEAST]
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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/dq/1dqx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1dqx ConSurf].
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<div style="clear:both"></div>
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'''CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)'''
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==See Also==
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*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5'-phosphate, at a resolution of 2.1 A and 2.4 A, respectively. Orotidine 5'-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5'-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favorable interactions with the phosphoryl group, the ribofuranosyl group, and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with developing negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition, H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
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[[Category: Large Structures]]
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==About this Structure==
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1DQX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA].
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==Reference==
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Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog., Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA, Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2011-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10681417 10681417]
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Hassell AM]]
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[[Category: Hassell, A M.]]
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[[Category: Milburn MV]]
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[[Category: Milburn, M V.]]
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[[Category: Miller BG]]
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[[Category: Miller, B G.]]
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[[Category: Short SA]]
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[[Category: Short, S A.]]
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[[Category: Wolfenden R]]
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[[Category: Wolfenden, R.]]
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[[Category: BMP]]
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[[Category: 6-hydroxyuridine 5'-phosphate]]
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[[Category: bmp]]
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[[Category: omp]]
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[[Category: orotidine 5'phosphate decarboxylase]]
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[[Category: tim barrel]]
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[[Category: ump]]
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[[Category: uridine 5'phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 11:32:59 2008''
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Current revision

CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)

PDB ID 1dqx

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