1dbt

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[[Image:1dbt.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP==
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The line below this paragraph, containing "STRUCTURE_1dbt", creates the "Structure Box" on the page.
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<StructureSection load='1dbt' size='340' side='right'caption='[[1dbt]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dbt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.4&#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=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
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{{STRUCTURE_1dbt| PDB=1dbt | SCENE= }}
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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=1dbt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbt OCA], [https://pdbe.org/1dbt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbt RCSB], [https://www.ebi.ac.uk/pdbsum/1dbt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbt ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP'''
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== Function ==
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[https://www.uniprot.org/uniprot/PYRF_BACSU PYRF_BACSU] 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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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The crystal structure of Bacillus subtilis orotidine 5'-monophosphate (OMP) decarboxylase with bound uridine 5'-monophosphate has been determined by multiple wavelength anomalous diffraction phasing techniques and refined to an R-factor of 19.3% at 2.4 A resolution. OMP decarboxylase is a dimer of two identical subunits. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. For each active site, most of the residues are contributed by one monomer with a few residues contributed from the adjacent monomer. The most highly conserved residues are located in the active site and suggest a novel catalytic mechanism for decarboxylation that is different from any previously proposed OMP decarboxylase mechanism. The uridine 5'-monophosphate molecule is bound to the active site such that the phosphate group is most exposed and the C5-C6 edge of the pyrimidine base is most buried. In the proposed catalytic mechanism, the ground state of the substrate is destabilized by electrostatic repulsion between the carboxylate of the substrate and the carboxylate of Asp60. This repulsion is reduced in the transition state by shifting negative charge from the carboxylate to C6 of the pyrimidine, which is close to the protonated amine of Lys62. We propose that the decarboxylation of OMP proceeds by an electrophilic substitution mechanism in which decarboxylation and carbon-carbon bond protonation by Lys62 occur in a concerted reaction.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/db/1dbt_consurf.spt"</scriptWhenChecked>
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1DBT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBT OCA].
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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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==Reference==
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</jmolCheckbox>
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The crystal structure and mechanism of orotidine 5'-monophosphate decarboxylase., Appleby TC, Kinsland C, Begley TP, Ealick SE, Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2005-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10681442 10681442]
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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=1dbt ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Orotidine-5'-phosphate decarboxylase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Appleby TC]]
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[[Category: Appleby, T C.]]
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[[Category: Begley TP]]
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[[Category: Begley, T P.]]
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[[Category: Ealick SE]]
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[[Category: Ealick, S E.]]
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[[Category: Kinsland CL]]
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[[Category: Kinsland, C L.]]
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[[Category: Decarboxylase]]
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[[Category: Tim barrel]]
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[[Category: Ump]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:40:02 2008''
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Current revision

CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH UMP

PDB ID 1dbt

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