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2azn

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(New page: 200px<br /><applet load="2azn" size="450" color="white" frame="true" align="right" spinBox="true" caption="2azn, resolution 2.7&Aring;" /> '''X-RAY Structure of 2,...)
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[[Image:2azn.gif|left|200px]]<br /><applet load="2azn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2azn, resolution 2.7&Aring;" />
 
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'''X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase'''<br />
 
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==Overview==
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==X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase==
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The pyrimidine reductase of the riboflavin biosynthetic pathway (MjaRED), specified by the open reading frame MJ0671 of Methanocaldococcus, jannaschii was expressed in Escherichia coli using a synthetic gene. The, synthetic open reading frame that was optimized for expression in E. coli, directed the synthesis of abundant amounts of the enzyme with an apparent, subunit mass of 25 kDa. The enzyme was purified to apparent homogeneity, and was shown to catalyze the conversion of, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into, 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate at a rate of, 0.8 micromol min(-1) mg(-1) at pH 8.0 and at 30 degrees C. The protein is, a homodimer as shown by sedimentation equilibrium analysis and sediments, at an apparent velocity of 3.5 S. The structure of the enzyme in complex, with the cofactor nicotinamide adenine dinucleotide phosphate was, determined by X-ray crystallography at a resolution of 2.5 Angstroms. The, folding pattern resembles that of dihydrofolate reductase with the, Thermotoga maritima ortholog as the most similar structure. The substrate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, was modeled, into the putative active site. The model suggests the transfer of the, pro-R hydrogen of C-4 of NADPH to C-1' of the substrate.
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<StructureSection load='2azn' size='340' side='right'caption='[[2azn]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2azn]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AZN 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]] 2.7&#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=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MA5:2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL'>MA5</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=2azn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2azn OCA], [https://pdbe.org/2azn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2azn RCSB], [https://www.ebi.ac.uk/pdbsum/2azn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2azn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RIB7_METJA RIB7_METJA] Catalyzes an early step in riboflavin biosynthesis, the NAD(P)H-dependent reduction of the ribose side chain of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, yielding 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate. The beta anomer is the authentic substrate, and the alpha anomer can serve as substrate subsequent to spontaneous anomerization. NADPH and NADH function equally well as the reductants. Does not catalyze the reduction of 5-amino-6-(5-phospho-D-ribosylamino)uracil to 5-amino-6-(5-phospho-D-ribitylamino)uracil.<ref>PMID:11889103</ref> <ref>PMID:18671734</ref>
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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/az/2azn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2azn 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 pyrimidine reductase of the riboflavin biosynthetic pathway (MjaRED) specified by the open reading frame MJ0671 of Methanocaldococcus jannaschii was expressed in Escherichia coli using a synthetic gene. The synthetic open reading frame that was optimized for expression in E. coli directed the synthesis of abundant amounts of the enzyme with an apparent subunit mass of 25 kDa. The enzyme was purified to apparent homogeneity and was shown to catalyze the conversion of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate into 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate at a rate of 0.8 micromol min(-1) mg(-1) at pH 8.0 and at 30 degrees C. The protein is a homodimer as shown by sedimentation equilibrium analysis and sediments at an apparent velocity of 3.5 S. The structure of the enzyme in complex with the cofactor nicotinamide adenine dinucleotide phosphate was determined by X-ray crystallography at a resolution of 2.5 Angstroms. The folding pattern resembles that of dihydrofolate reductase with the Thermotoga maritima ortholog as the most similar structure. The substrate, 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, was modeled into the putative active site. The model suggests the transfer of the pro-R hydrogen of C-4 of NADPH to C-1' of the substrate.
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==About this Structure==
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Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii.,Chatwell L, Krojer T, Fidler A, Romisch W, Eisenreich W, Bacher A, Huber R, Fischer M J Mol Biol. 2006 Jun 23;359(5):1334-51. Epub 2006 May 6. PMID:16730025<ref>PMID:16730025</ref>
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2AZN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with MA5, NAP and EPE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/5-amino-6-(5-phosphoribosylamino)uracil_reductase 5-amino-6-(5-phosphoribosylamino)uracil reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.193 1.1.1.193] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2AZN 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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Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of Methanocaldococcus jannaschii., Chatwell L, Krojer T, Fidler A, Romisch W, Eisenreich W, Bacher A, Huber R, Fischer M, J Mol Biol. 2006 Jun 23;359(5):1334-51. Epub 2006 May 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16730025 16730025]
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</div>
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[[Category: 5-amino-6-(5-phosphoribosylamino)uracil reductase]]
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<div class="pdbe-citations 2azn" 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>
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[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Methanocaldococcus jannaschii]]
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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: Chatwell L]]
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[[Category: Chatwell, L.]]
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[[Category: Fischer M]]
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[[Category: Fischer, M.]]
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[[Category: Huber R]]
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[[Category: Huber, R.]]
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[[Category: Krojer T]]
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[[Category: Krojer, T.]]
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[[Category: EPE]]
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[[Category: MA5]]
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[[Category: NAP]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 08:28:54 2007''
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Current revision

X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase

PDB ID 2azn

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