1l2u

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(New page: 200px<br /><applet load="1l2u" size="450" color="white" frame="true" align="right" spinBox="true" caption="1l2u, resolution 2.5&Aring;" /> '''Orotidine 5'-monophos...)
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[[Image:1l2u.jpg|left|200px]]<br /><applet load="1l2u" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1l2u, resolution 2.5&Aring;" />
 
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'''Orotidine 5'-monophosphate decarboxylase from E. coli'''<br />
 
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==Overview==
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==Orotidine 5'-monophosphate decarboxylase from E. coli==
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Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the, decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate, (UMP). We have earlier determined the structure of ODCase from Escherichia, coli complexed with the inhibitor, 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid (BMP); here we present, the 2.5 A structure of the uncomplexed apo enzyme, determined from twinned, crystals. A structural analysis and comparison of the two structures of, the E. coli enzyme show that binding of the inhibitor is accompanied by, significant domain movements of approximately 12 degrees around a hinge, that crosses the active site. Hence, the ODCase dimer, which contains two, active sites, may be divided in three domains: a central domain that is, fixed, and two lids which independently move 12 degrees upon binding., Corresponding analyses, presented herein, of the two Saccharomyces, cerevisiae ODCase structures (with and without BMP) and the, Methanobacterium thermoautotrophicum ODCase structures (with and without, 6-aza UMP) show very similar, but somewhat smaller domain movements. The, domain movements seem to be initiated by the phosphoryl binding to the, enzyme and can explain why the binding of the phosphoryl group is, essential for the catalytic function.
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<StructureSection load='1l2u' size='340' side='right'caption='[[1l2u]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1l2u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L2U 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]] 2.5&#8491;</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=1l2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l2u OCA], [https://pdbe.org/1l2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l2u RCSB], [https://www.ebi.ac.uk/pdbsum/1l2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l2u ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]
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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/l2/1l2u_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=1l2u 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) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate (UMP). We have earlier determined the structure of ODCase from Escherichia coli complexed with the inhibitor 1-(5'-phospho-beta-d-ribofuranosyl)barbituric acid (BMP); here we present the 2.5 A structure of the uncomplexed apo enzyme, determined from twinned crystals. A structural analysis and comparison of the two structures of the E. coli enzyme show that binding of the inhibitor is accompanied by significant domain movements of approximately 12 degrees around a hinge that crosses the active site. Hence, the ODCase dimer, which contains two active sites, may be divided in three domains: a central domain that is fixed, and two lids which independently move 12 degrees upon binding. Corresponding analyses, presented herein, of the two Saccharomyces cerevisiae ODCase structures (with and without BMP) and the Methanobacterium thermoautotrophicum ODCase structures (with and without 6-aza UMP) show very similar, but somewhat smaller domain movements. The domain movements seem to be initiated by the phosphoryl binding to the enzyme and can explain why the binding of the phosphoryl group is essential for the catalytic function.
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==About this Structure==
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Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase.,Harris P, Poulsen JC, Jensen KF, Larsen S J Mol Biol. 2002 May 10;318(4):1019-29. PMID:12054799<ref>PMID:12054799</ref>
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1L2U is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. 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=1L2U 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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Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase., Harris P, Poulsen JC, Jensen KF, Larsen S, J Mol Biol. 2002 May 10;318(4):1019-29. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12054799 12054799]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1l2u" 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: Harris, P.]]
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[[Category: Jensen, K.F.]]
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[[Category: Larsen, S.]]
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[[Category: Poulsen, J.C.]]
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[[Category: beta-alpha-barrel]]
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[[Category: homodimer]]
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[[Category: twinned crystals]]
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[[Category: x-ray diffraction]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:12:03 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: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Harris P]]
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[[Category: Jensen KF]]
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[[Category: Larsen S]]
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[[Category: Poulsen JC]]

Current revision

Orotidine 5'-monophosphate decarboxylase from E. coli

PDB ID 1l2u

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