1jjk: Difference between revisions

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-[[Image:1jjk.gif|left|200px]]
- {{Structure
+==Selenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli Causes a Change in Crystal Contacts and Space Group==
-|PDB= 1jjk |SIZE=350|CAPTION= <scene name='initialview01'>1jjk</scene>, resolution 3.&Aring;
+<StructureSection load='1jjk' size='340' side='right'caption='[[1jjk]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BMP:6-HYDROXYURIDINE-5'-PHOSPHATE'>BMP</scene>
+<table><tr><td colspan='2'>[[1jjk]] is a 16 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=1JJK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JJK FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
-|GENE=
+<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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jjk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jjk OCA], [https://pdbe.org/1jjk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jjk RCSB], [https://www.ebi.ac.uk/pdbsum/1jjk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jjk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jj/1jjk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1jjk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in the de novo biosynthesis of uridine 5'-monophosphate. In order to determine the structure of ODCase from Escherichia coli by the multi-wavelength anomalous dispersion technique, both native and SeMet-substituted proteins have been produced and purified. During the production of SeMet ODCase, it was observed that SeMet was the only amino acid that it was necessary to add to the defined medium during expression. SeMet-substituted ODCase in complex with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid crystallizes under similar conditions as the native enzyme. In contrast to the native enzyme, where the crystals belong to the orthorhombic space group P2(1)2(1)2(1), the SeMet-substituted enzyme crystallizes in the monoclinic space group P2(1), with a quadrupling of the volume of the asymmetric unit. Despite the drastic difference in symmetry, the overall crystal packing is effectively identical in the two crystal forms. The change in space group appears to originate in differences in the crystal contacts near the SeMet and Met residues. These differences can be rationalized in terms of SeMet's larger size and hydrophobicity.
-'''Selenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli Causes a Change in Crystal Contacts and Space Group'''
+Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group.,Poulsen JC, Harris P, Jensen KF, Larsen S Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1251-9. Epub 2001, Aug 23. PMID:11526316<ref>PMID:11526316</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1jjk" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in the de novo biosynthesis of uridine 5'-monophosphate. In order to determine the structure of ODCase from Escherichia coli by the multi-wavelength anomalous dispersion technique, both native and SeMet-substituted proteins have been produced and purified. During the production of SeMet ODCase, it was observed that SeMet was the only amino acid that it was necessary to add to the defined medium during expression. SeMet-substituted ODCase in complex with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid crystallizes under similar conditions as the native enzyme. In contrast to the native enzyme, where the crystals belong to the orthorhombic space group P2(1)2(1)2(1), the SeMet-substituted enzyme crystallizes in the monoclinic space group P2(1), with a quadrupling of the volume of the asymmetric unit. Despite the drastic difference in symmetry, the overall crystal packing is effectively identical in the two crystal forms. The change in space group appears to originate in differences in the crystal contacts near the SeMet and Met residues. These differences can be rationalized in terms of SeMet's larger size and hydrophobicity.
+*[[Uridine 5'-monophosphate synthase 3D structures|Uridine 5'-monophosphate synthase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-JJK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JJK OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group., Poulsen JC, Harris P, Jensen KF, Larsen S, Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1251-9. Epub 2001, Aug 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11526316 11526316]
 [[Category: Escherichia coli]]
-[[Category: Orotidine-5'-phosphate decarboxylase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Harris P]]
-[[Category: Harris, P.]]
+[[Category: Jensen KF]]
-[[Category: Jensen, K F.]]
+[[Category: Larsen S]]
-[[Category: Larsen, S.]]
+[[Category: Poulsen J-CN]]
-[[Category: Poulsen, J C.N.]]
-[[Category: BMP]]
-[[Category: alpha-beta-barrel]]
-[[Category: homodimer]]
-[[Category: protein-inhibitor complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:04:18 2008''