2cbn

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[[Image:2cbn.gif|left|200px]]<br /><applet load="2cbn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2cbn, resolution 2.9&Aring;" />
 
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'''CRYSTAL STRUCTURE OF ZIPD FROM ESCHERICHIA COLI'''<br />
 
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==Overview==
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==Crystal structure of ZipD from Escherichia coli==
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The elaC gene product from Escherichia coli, ZiPD, is a 3' tRNA-processing, endonuclease belonging to the tRNase Z family of enzymes that have been, identified in a wide variety of organisms. In contrast to the elaC, homologue from Bacillus subtilis, E. coli elaC is not essential for, viability, and although both enzymes process only precursor tRNA, (pre-tRNA) lacking a CCA triplet at the 3' end in vitro, the physiological, role of ZiPD remains enigmatic because all pre-tRNA species in E. coli are, transcribed with the CCA triplet. We present the first crystal structure, of ZiPD determined by multiple anomalous diffraction at a resolution of, 2.9 A. This structure shares many features with the tRNase Z enzymes from, B. subtilis and Thermotoga maritima, but there are distinct differences in, metal binding and overall domain organization. Unlike the previously, described homologous structures, ZiPD dimers display crystallographic, symmetry and fully loaded metal sites. The ZiPD exosite is similar to that, of the B. subtilis enzyme structurally, but its position with respect to, the protein core differs substantially, illustrating its ability to act as, a clamp in binding tRNA. Furthermore, the ZiPD crystal structure presented, here provides insight into the enzyme's cooperativity and assists the, ongoing attempt to elucidate the physiological function of this protein.
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<StructureSection load='2cbn' size='340' side='right'caption='[[2cbn]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2cbn]] is a 1 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=2CBN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CBN 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]] 2.9&#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=ZN:ZINC+ION'>ZN</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=2cbn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cbn OCA], [https://pdbe.org/2cbn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cbn RCSB], [https://www.ebi.ac.uk/pdbsum/2cbn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cbn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RBN_ECOLI RBN_ECOLI] Zinc phosphodiesterase, which has both exoribonuclease and endoribonuclease activities, depending on the nature of the substrate and of the added divalent cation, and on its 3'-terminal structure. Can process the 3' termini of both CCA-less and CCA-containing tRNA precursors. CCA-less tRNAs are cleaved endonucleolytically after the discriminator base, whereas residues following the CCA sequence can be removed exonucleolytically or endonucleolytically in CCA-containing molecules. Does not remove the CCA sequence. May also be involved in the degradation of mRNAs. In vitro, hydrolyzes bis(p-nitrophenyl)phosphate and thymidine-5'-p-nitrophenyl phosphate.<ref>PMID:12029081</ref> <ref>PMID:15764599</ref> <ref>PMID:16629673</ref> <ref>PMID:19366704</ref> <ref>PMID:20489203</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/cb/2cbn_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=2cbn 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 elaC gene product from Escherichia coli, ZiPD, is a 3' tRNA-processing endonuclease belonging to the tRNase Z family of enzymes that have been identified in a wide variety of organisms. In contrast to the elaC homologue from Bacillus subtilis, E. coli elaC is not essential for viability, and although both enzymes process only precursor tRNA (pre-tRNA) lacking a CCA triplet at the 3' end in vitro, the physiological role of ZiPD remains enigmatic because all pre-tRNA species in E. coli are transcribed with the CCA triplet. We present the first crystal structure of ZiPD determined by multiple anomalous diffraction at a resolution of 2.9 A. This structure shares many features with the tRNase Z enzymes from B. subtilis and Thermotoga maritima, but there are distinct differences in metal binding and overall domain organization. Unlike the previously described homologous structures, ZiPD dimers display crystallographic symmetry and fully loaded metal sites. The ZiPD exosite is similar to that of the B. subtilis enzyme structurally, but its position with respect to the protein core differs substantially, illustrating its ability to act as a clamp in binding tRNA. Furthermore, the ZiPD crystal structure presented here provides insight into the enzyme's cooperativity and assists the ongoing attempt to elucidate the physiological function of this protein.
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==About this Structure==
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The crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins.,Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W J Bacteriol. 2006 Feb;188(4):1607-14. PMID:16452444<ref>PMID:16452444</ref>
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2CBN 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 ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_Z Ribonuclease Z], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.11 3.1.26.11] Known structural/functional Site: <scene name='pdbsite=AC1:Zn Binding Site For Chain A'>AC1</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2CBN 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 crystal structure of the zinc phosphodiesterase from Escherichia coli provides insight into function and cooperativity of tRNase Z-family proteins., Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W, J Bacteriol. 2006 Feb;188(4):1607-14. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16452444 16452444]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 2cbn" style="background-color:#fffaf0;"></div>
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[[Category: Ribonuclease Z]]
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[[Category: Single protein]]
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[[Category: Kostelecky, B.]]
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[[Category: Meyer-Klaucke, W.]]
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[[Category: Pohl, E.]]
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[[Category: ZN]]
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[[Category: endonuclease]]
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[[Category: hydrolase]]
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[[Category: metal-binding]]
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[[Category: phosphodiesterase beta lactamase trnase z]]
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[[Category: trna processing]]
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[[Category: zinc]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 19:16:55 2007''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 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: Escherichia coli]]
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[[Category: Large Structures]]
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[[Category: Kostelecky B]]
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[[Category: Meyer-Klaucke W]]
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[[Category: Pohl E]]

Current revision

Crystal structure of ZipD from Escherichia coli

PDB ID 2cbn

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