1fsi

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(New page: 200px<br /><applet load="1fsi" size="450" color="white" frame="true" align="right" spinBox="true" caption="1fsi, resolution 2.50&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1fsi.gif|left|200px]]<br /><applet load="1fsi" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1fsi, resolution 2.50&Aring;" />
 
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'''CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA==
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The crystal structure of the cyclic phosphodiesterase (CPDase) from, Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was, determined at 2.5 A resolution. CPDase hydrolyzes ADP-ribose 1",2"-cyclic, phosphate (Appr&gt;p), a product of the tRNA splicing reaction, to the, monoester ADP-ribose 1"-phosphate (Appr-1"p). The 181 amino acid protein, shows a novel, bilobal arrangement of two alphabeta modules. Each lobe, consists of two alpha-helices on the outer side of the molecule, framing a, three- or four-stranded antiparallel beta-sheet in the core of the, protein. The active site is formed at the interface of the two beta-sheets, in a water-filled cavity involving residues from two H-X-T/S-X motifs., This previously noticed motif participates in coordination of a sulfate, ion. A solvent-exposed surface loop (residues 100-115) is very likely to, play a flap-like role, opening and closing the active site. Based on the, crystal structure and on recent mutagenesis studies of a homologous CPDase, from Saccharomyces cerevisiae, we propose an enzymatic mechanism that, employs the nucleophilic attack of a water molecule activated by one of, the active site histidines.
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<StructureSection load='1fsi' size='340' side='right'caption='[[1fsi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1fsi]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FSI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FSI 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1fsi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fsi OCA], [https://pdbe.org/1fsi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fsi RCSB], [https://www.ebi.ac.uk/pdbsum/1fsi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fsi ProSAT]</span></td></tr>
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</table>
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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/fs/1fsi_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=1fsi 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 crystal structure of the cyclic phosphodiesterase (CPDase) from Arabidopsis thaliana, an enzyme involved in the tRNA splicing pathway, was determined at 2.5 A resolution. CPDase hydrolyzes ADP-ribose 1",2"-cyclic phosphate (Appr&gt;p), a product of the tRNA splicing reaction, to the monoester ADP-ribose 1"-phosphate (Appr-1"p). The 181 amino acid protein shows a novel, bilobal arrangement of two alphabeta modules. Each lobe consists of two alpha-helices on the outer side of the molecule, framing a three- or four-stranded antiparallel beta-sheet in the core of the protein. The active site is formed at the interface of the two beta-sheets in a water-filled cavity involving residues from two H-X-T/S-X motifs. This previously noticed motif participates in coordination of a sulfate ion. A solvent-exposed surface loop (residues 100-115) is very likely to play a flap-like role, opening and closing the active site. Based on the crystal structure and on recent mutagenesis studies of a homologous CPDase from Saccharomyces cerevisiae, we propose an enzymatic mechanism that employs the nucleophilic attack of a water molecule activated by one of the active site histidines.
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==About this Structure==
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Structure and mechanism of activity of the cyclic phosphodiesterase of Appr&gt;p, a product of the tRNA splicing reaction.,Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A EMBO J. 2000 Nov 15;19(22):6207-17. PMID:11080166<ref>PMID:11080166</ref>
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1FSI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1FSI 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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Structure and mechanism of activity of the cyclic phosphodiesterase of Appr&gt;p, a product of the tRNA splicing reaction., Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A, EMBO J. 2000 Nov 15;19(22):6207-17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11080166 11080166]
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</div>
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[[Category: Arabidopsis thaliana]]
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<div class="pdbe-citations 1fsi" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Filipowicz, W.]]
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[[Category: Genschik, P.]]
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[[Category: Hofmann, A.]]
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[[Category: Ruvinov, S.]]
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[[Category: Wlodawer, A.]]
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[[Category: Zdanov, A.]]
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[[Category: SO4]]
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[[Category: 2']]
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[[Category: 2''-cyclic phosphate]]
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[[Category: 3'-cyclic nucleotide phosphodiesterase]]
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[[Category: adp-ribose 1'']]
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[[Category: appr>p]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:14:27 2007''
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==See Also==
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 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: Arabidopsis thaliana]]
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[[Category: Large Structures]]
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[[Category: Filipowicz W]]
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[[Category: Genschik P]]
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[[Category: Hofmann A]]
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[[Category: Ruvinov S]]
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[[Category: Wlodawer A]]
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[[Category: Zdanov A]]

Current revision

CRYSTAL STRUCTURE OF CYCLIC NUCLEOTIDE PHOSPHODIESTERASE OF APPR>P FROM ARABIDOPSIS THALIANA

PDB ID 1fsi

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