2dkf

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[[Image:2dkf.jpg|left|200px]]
 
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{{Structure
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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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|PDB= 2dkf |SIZE=350|CAPTION= <scene name='initialview01'>2dkf</scene>, resolution 2.8&Aring;
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<StructureSection load='2dkf' size='340' side='right'caption='[[2dkf]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
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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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|ACTIVITY=
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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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|GENE= TTHA0252 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
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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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}}
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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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'''Crystal Structure of TTHA0252 from Thermus thermophilus HB8, a RNA Degradation Protein of the Metallo-beta-lactamase Superfamily'''
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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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==Overview==
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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 ==
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.
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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==About this Structure==
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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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2DKF is a [[Single protein]] structure of sequence 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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==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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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:[http://www.ncbi.nlm.nih.gov/pubmed/16945939 16945939]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2dkf" style="background-color:#fffaf0;"></div>
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[[Category: Thermus thermophilus]]
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[[Category: Ishikawa, I.]]
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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: ZN]]
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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 Thu Mar 20 16:28:14 2008''
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==See Also==
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*[[Beta-lactamase 3D structures|Beta-lactamase 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: Large Structures]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Ishikawa I]]
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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: Yokoyama S]]

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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