2e6y

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(New page: 200px<br /><applet load="2e6y" size="450" color="white" frame="true" align="right" spinBox="true" caption="2e6y, resolution 1.60&Aring;" /> '''Covalent complex of ...)
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[[Image:2e6y.gif|left|200px]]<br /><applet load="2e6y" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2e6y, resolution 1.60&Aring;" />
 
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'''Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP'''<br />
 
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==Overview==
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==Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP==
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Orotidine 5'-monophosphate decarboxylase (ODCase) has evolved to catalyze, the decarboxylation of orotidine 5'-monophosphate without any covalent, intermediates. Active site residues in ODCase are involved in an extensive, hydrogen-bonding network. We discovered that 6-iodouridine, 5'-monophosphate (6-iodo-UMP) irreversibly inhibits the catalytic, activities of ODCases from Methanobacterium thermoautotrophicum and, Plasmodium falciparum. Mass spectral analysis of the enzyme-inhibitor, complex confirms covalent attachment of the inhibitor to ODCase, accompanied by the loss of two protons and the iodo moiety. The X-ray, crystal structure (1.6 A resolution) of the complex of the inhibitor and, ODCase clearly shows the covalent bond formation with the active site, Lys-42 residue. 6-Iodo-UMP inhibits ODCase in a time- and, concentration-dependent fashion. 6-Iodouridine, the nucleoside form of, 6-iodo-UMP, exhibited potent antiplasmodial activity, with IC50s of 4.4, +/- 1.3 muM and 6.2 +/- 0.7 muM against P. falciparum ItG and 3D7, isolates, respectively. 6-Iodouridine 5'-monophosphate is a novel covalent, inhibitor of ODCase, and its nucleoside analogue paves the way to a new, class of inhibitors against malaria.
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<StructureSection load='2e6y' size='340' side='right'caption='[[2e6y]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2e6y]] is a 2 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>
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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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
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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=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [https://pdbe.org/2e6y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [https://www.ebi.ac.uk/pdbsum/2e6y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e6y ProSAT]</span></td></tr>
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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/e6/2e6y_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=2e6y 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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Orotidine 5'-monophosphate decarboxylase (ODCase) has evolved to catalyze the decarboxylation of orotidine 5'-monophosphate without any covalent intermediates. Active site residues in ODCase are involved in an extensive hydrogen-bonding network. We discovered that 6-iodouridine 5'-monophosphate (6-iodo-UMP) irreversibly inhibits the catalytic activities of ODCases from Methanobacterium thermoautotrophicum and Plasmodium falciparum. Mass spectral analysis of the enzyme-inhibitor complex confirms covalent attachment of the inhibitor to ODCase accompanied by the loss of two protons and the iodo moiety. The X-ray crystal structure (1.6 A resolution) of the complex of the inhibitor and ODCase clearly shows the covalent bond formation with the active site Lys-72 [corrected] residue. 6-Iodo-UMP inhibits ODCase in a time- and concentration-dependent fashion. 6-Iodouridine, the nucleoside form of 6-iodo-UMP, exhibited potent antiplasmodial activity, with IC50s of 4.4 +/- 1.3 microM and 6.2 +/- 0.7 microM against P. falciparum ItG and 3D7 isolates, respectively. 6-Iodouridine 5'-monophosphate is a novel covalent inhibitor of ODCase, and its nucleoside analogue paves the way to a new class of inhibitors against malaria.
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==About this Structure==
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A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity.,Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP J Med Chem. 2007 Mar 8;50(5):915-21. Epub 2007 Feb 10. PMID:17290979<ref>PMID:17290979</ref>
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2E6Y 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 U5P and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. 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=2E6Y OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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A Potent, Covalent Inhibitor of Orotidine 5'-Monophosphate Decarboxylase with Antimalarial Activity., Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP, J Med Chem. 2007 Mar 8;50(5):915-921. Epub 2007 Feb 10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17290979 17290979]
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</div>
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[[Category: Methanothermobacter thermautotrophicus]]
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<div class="pdbe-citations 2e6y" style="background-color:#fffaf0;"></div>
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Single protein]]
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[[Category: Bello, A.M.]]
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[[Category: Fujihashi, M.]]
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[[Category: Kotra, L.P.]]
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[[Category: Pai, E.F.]]
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[[Category: GOL]]
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[[Category: U5P]]
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[[Category: tim-barrel]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:58:13 2007''
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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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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Methanothermobacter thermautotrophicus]]
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[[Category: Bello AM]]
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[[Category: Fujihashi M]]
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[[Category: Kotra LP]]
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[[Category: Pai EF]]

Current revision

Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP

PDB ID 2e6y

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