2dkf

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{{Seed}}
 
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[[Image:2dkf.png|left|200px]]
 
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==Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily==
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The line below this paragraph, containing "STRUCTURE_2dkf", creates the "Structure Box" on the page.
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<StructureSection load='2dkf' size='340' side='right'caption='[[2dkf]], [[Resolution|resolution]] 2.80&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'>[[2dkf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DKF 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]] 2.8&#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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2dkf| PDB=2dkf | 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=2dkf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dkf OCA], [https://pdbe.org/2dkf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dkf RCSB], [https://www.ebi.ac.uk/pdbsum/2dkf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dkf ProSAT], [https://www.topsan.org/Proteins/RSGI/2dkf TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNSE_THET8 RNSE_THET8] Has endoribonuclease activity towards 23S and 16S rRNA (in vitro).
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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/dk/2dkf_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=2dkf 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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In bacterial RNA metabolism, mRNA degradation is an important process for gene expression. Recently, a novel ribonuclease (RNase), belonging to the beta-CASP family within the metallo-beta-lactamase superfamily, was identified as a functional homologue of RNase E, a major component for mRNA degradation in Escherichia coli. Here, we have determined the crystal structure of TTHA0252 from Thermus thermophilus HB8, which represents the first report of the tertiary structure of a beta-CASP family protein. TTHA0252 comprises two separate domains: a metallo-beta-lactamase domain and a "clamp" domain. The active site of the enzyme is located in a cleft between the two domains, which includes two zinc ions coordinated by seven conserved residues. Although this configuration is similar to those of other beta-lactamases, TTHA0252 has one conserved His residue characteristic of the beta-CASP family as a ligand. We also detected nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results reveal structural and functional aspects of novel RNase E-like enzymes with a beta-CASP fold.
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===Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily===
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Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily.,Ishikawa H, Nakagawa N, Kuramitsu S, Masui R J Biochem. 2006 Oct;140(4):535-42. Epub 2006 Aug 31. PMID:16945939<ref>PMID:16945939</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2dkf" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_16945939}}, adds the Publication Abstract to the page
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*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 16945939 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16945939}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2DKF is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DKF OCA].
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[[Category: Thermus thermophilus HB8]]
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[[Category: Ishikawa I]]
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==Reference==
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[[Category: Kuramitsu S]]
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<ref group="xtra">PMID:16945939</ref><references group="xtra"/>
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[[Category: Masui R]]
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[[Category: Thermus thermophilus]]
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[[Category: Nakagawa N]]
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[[Category: Ishikawa, I.]]
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[[Category: Yokoyama S]]
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[[Category: Kuramitsu, S.]]
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[[Category: Masui, R.]]
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[[Category: Nakagawa, N.]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama, S.]]
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[[Category: Beta-casp family]]
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[[Category: Metallo-beta-lactamase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Ribonuclease]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rnase e]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Thermus thermophilus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:07:02 2009''
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Current revision

Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily

PDB ID 2dkf

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