1pkv

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(New page: 200px<br /><applet load="1pkv" size="450" color="white" frame="true" align="right" spinBox="true" caption="1pkv, resolution 2.60&Aring;" /> '''The N-terminal domai...)
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[[Image:1pkv.jpg|left|200px]]<br /><applet load="1pkv" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pkv, resolution 2.60&Aring;" />
 
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'''The N-terminal domain of riboflavin synthase in complex with riboflavin'''<br />
 
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==Overview==
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==The N-terminal domain of riboflavin synthase in complex with riboflavin==
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Riboflavin synthase of Escherichia coli is a homotrimer with a molecular, mass of 70 kDa. The enzyme catalyzes the dismutation of, 6,7-dimethyl-8-(1'-D-ribityl)-lumazine, affording riboflavin and, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. The N-terminal segment, (residues 1-87) and the C-terminal segment (residues 98-187) form, beta-barrels with similar fold and a high degree of sequence similarity. A, recombinant peptide comprising amino acid residues 1-97 forms a dimer, which binds riboflavin with high affinity. Here, we report the structure, of this construct in complex with riboflavin at 2.6A resolution. It is, demonstrated that the complex can serve as a model for ligand-binding in, the native enzyme. The structure and riboflavin-binding mode is in, excellent agreement with structural information obtained from the native, enzyme from Escherichia coli and riboflavin synthase from, Schizosaccharomyces pombe. The implications for the binding specificity, and the regiospecificity of the catalyzed reaction are discussed.
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<StructureSection load='1pkv' size='340' side='right'caption='[[1pkv]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1pkv]] 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=1PKV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PKV 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]] 2.6&#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=RBF:RIBOFLAVIN'>RBF</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=1pkv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pkv OCA], [https://pdbe.org/1pkv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pkv RCSB], [https://www.ebi.ac.uk/pdbsum/1pkv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pkv ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RISA_ECOLI RISA_ECOLI] Catalyzes the dismutation of two molecules of 6,7-dimethyl-8-ribityllumazine, resulting in the formation of riboflavin and 5-amino-6-(D-ribitylamino)uracil.
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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/pk/1pkv_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=1pkv 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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Riboflavin synthase of Escherichia coli is a homotrimer with a molecular mass of 70 kDa. The enzyme catalyzes the dismutation of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine, affording riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. The N-terminal segment (residues 1-87) and the C-terminal segment (residues 98-187) form beta-barrels with similar fold and a high degree of sequence similarity. A recombinant peptide comprising amino acid residues 1-97 forms a dimer, which binds riboflavin with high affinity. Here, we report the structure of this construct in complex with riboflavin at 2.6A resolution. It is demonstrated that the complex can serve as a model for ligand-binding in the native enzyme. The structure and riboflavin-binding mode is in excellent agreement with structural information obtained from the native enzyme from Escherichia coli and riboflavin synthase from Schizosaccharomyces pombe. The implications for the binding specificity and the regiospecificity of the catalyzed reaction are discussed.
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==About this Structure==
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The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution.,Meining W, Eberhardt S, Bacher A, Ladenstein R J Mol Biol. 2003 Aug 29;331(5):1053-63. PMID:12927541<ref>PMID:12927541</ref>
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1PKV is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with RBF as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Riboflavin_synthase Riboflavin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.9 2.5.1.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PKV 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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The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution., Meining W, Eberhardt S, Bacher A, Ladenstein R, J Mol Biol. 2003 Aug 29;331(5):1053-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12927541 12927541]
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</div>
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<div class="pdbe-citations 1pkv" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Riboflavin synthase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Bacher A]]
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[[Category: Bacher, A.]]
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[[Category: Eberhardt S]]
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[[Category: Eberhardt, S.]]
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[[Category: Ladenstein R]]
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[[Category: Ladenstein, R.]]
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[[Category: Meining W]]
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[[Category: Meining, W.]]
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[[Category: RBF]]
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[[Category: beta-barrel]]
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[[Category: dimer]]
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[[Category: greek key motif]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:54:01 2007''
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Current revision

The N-terminal domain of riboflavin synthase in complex with riboflavin

PDB ID 1pkv

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