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1km2

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[[Image:1km2.gif|left|200px]]<br /><applet load="1km2" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1km2, resolution 1.50&Aring;" />
 
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'''crystal structure of orotidine monophosphate mutant Q185A with 6-azaUMP'''<br />
 
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==Overview==
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==crystal structure of orotidine monophosphate mutant Q185A with 6-azaUMP==
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The crystal structures of orotidine 5'-monophosphate decarboxylases from four different sources have been published recently. However, the detailed mechanism of catalysis of the most proficient enzyme known to date remains elusive. As the ligand-protein interactions at the orotate binding site are crucial to the understanding of this enzyme, we mutated several of the residues surrounding the aromatic part of the substrate, individually and in combination. The ensuing effects on enzyme structure and stability were characterized by X-ray crystallography of inhibitor, product, or substrate complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B being charged and forming an 'alternate charge network' around the reactive part of the substrate. In addition to exerting charge-charge repulsion on the orotate carboxylate, Asp70 also makes a crucial contribution to enzyme stability. Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding.
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<StructureSection load='1km2' size='340' side='right'caption='[[1km2]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1km2]] is a 1 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=1KM2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KM2 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]] 1.5&#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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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1km2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km2 OCA], [https://pdbe.org/1km2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1km2 RCSB], [https://www.ebi.ac.uk/pdbsum/1km2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1km2 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/km/1km2_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=1km2 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KM2 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 <scene name='pdbligand=UP6:'>UP6</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM2 OCA].
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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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==Reference==
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</StructureSection>
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Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography., Wu N, Gillon W, Pai EF, Biochemistry. 2002 Mar 26;41(12):4002-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11900543 11900543]
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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: Gillon W]]
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[[Category: Single protein]]
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[[Category: Pai EF]]
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[[Category: Gillon, W.]]
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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: tim barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:35:33 2008''
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Current revision

crystal structure of orotidine monophosphate mutant Q185A with 6-azaUMP

PDB ID 1km2

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