3lty

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{{STRUCTURE_3lty| PDB=3lty | SCENE= }}
 
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===Crystal structure of the mutant V182A,I218A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===
 
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{{ABSTRACT_PUBMED_20369850}}
 
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==Function==
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==Crystal structure of the mutant V182A,I218A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
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[[http://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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<StructureSection load='3lty' size='340' side='right'caption='[[3lty]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3lty]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LTY 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=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</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=3lty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lty OCA], [https://pdbe.org/3lty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lty RCSB], [https://www.ebi.ac.uk/pdbsum/3lty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lty 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/lt/3lty_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=3lty 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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The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.
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==About this Structure==
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Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.,Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850<ref>PMID:20369850</ref>
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[[3lty]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LTY 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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<ref group="xtra">PMID:020369850</ref><references group="xtra"/><references/>
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</div>
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[[Category: Methanothermobacter thermautotrophicus]]
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<div class="pdbe-citations 3lty" style="background-color:#fffaf0;"></div>
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Almo, S C.]]
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==See Also==
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[[Category: Fedorov, A A.]]
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*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
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[[Category: Fedorov, E V.]]
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== References ==
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[[Category: Gerlt, J A.]]
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<references/>
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[[Category: Wood, B M.]]
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__TOC__
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[[Category: Decarboxylase]]
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</StructureSection>
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[[Category: Inhibitor bmp]]
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[[Category: Large Structures]]
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[[Category: Lyase]]
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[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
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[[Category: Mutant v182a i218a]]
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[[Category: Almo SC]]
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[[Category: Pyrimidine biosynthesis]]
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[[Category: Fedorov AA]]
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[[Category: Fedorov EV]]
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[[Category: Gerlt JA]]
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[[Category: Wood BM]]

Current revision

Crystal structure of the mutant V182A,I218A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

PDB ID 3lty

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