1dvj

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(New page: 200px<br /><applet load="1dvj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dvj, resolution 1.50&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1dvj.jpg|left|200px]]<br /><applet load="1dvj" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dvj, resolution 1.50&Aring;" />
 
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'''CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP==
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Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of, orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in, biosynthesis of pyrimidine nucleotides. As part of a Structural Genomics, Initiative, the crystal structures of the ligand-free and the6-azauridine, 5'-monophosphate-complexed forms have been determined at 1.8 and 1.5 A, respectively. The protein assumes a TIM-barrel fold with one side of the, barrel closed off and the other side binding the inhibitor. A unique array, of alternating charges (Lys-Asp-Lys-Asp) in the active site prompted us to, apply quantum mechanical and molecular dynamics calculations to analyze, the relative contributions of ground state destabilization and transition, state stabilization to catalysis. The remarkable catalytic power of, orotidine 5'-monophosphate decarboxylase is almost exclusively achieved, via destabilization of the reactive part of the substrate, which is, compensated for by strong binding of the phosphate and ribose groups. The, computational results are consistent with a catalytic mechanism that is, characterized by Jencks's Circe effect.
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<StructureSection load='1dvj' size='340' side='right'caption='[[1dvj]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dvj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DVJ FirstGlance]. <br>
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1DVJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus] with UP6 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DVJ OCA].
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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]] 1.5&#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=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
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==Reference==
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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=1dvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dvj OCA], [https://pdbe.org/1dvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dvj RCSB], [https://www.ebi.ac.uk/pdbsum/1dvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dvj ProSAT]</span></td></tr>
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Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase., Wu N, Mo Y, Gao J, Pai EF, Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2017-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10681441 10681441]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
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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/dv/1dvj_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=1dvj ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Methanothermobacter thermautotrophicus]]
[[Category: Methanothermobacter thermautotrophicus]]
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Gao J]]
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[[Category: Single protein]]
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[[Category: Mo Y]]
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[[Category: Gao, J.]]
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[[Category: Pai EF]]
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[[Category: Mo, Y.]]
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[[Category: Wu N]]
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[[Category: Pai, E.F.]]
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[[Category: Wu, N.]]
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[[Category: UP6]]
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[[Category: dimer]]
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[[Category: tim barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:37:21 2007''
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Current revision

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

PDB ID 1dvj

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