1z3a: Difference between revisions

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 ==Crystal structure of tRNA adenosine deaminase TadA from Escherichia coli==
-<StructureSection load='1z3a' size='340' side='right' caption='[[1z3a]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
+<StructureSection load='1z3a' size='340' side='right'caption='[[1z3a]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1z3a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z3A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Z3A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1z3a]] is a 2 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=1Z3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Z3A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tada ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z3a OCA], [http://pdbe.org/1z3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1z3a RCSB], [http://www.ebi.ac.uk/pdbsum/1z3a PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/1z3a TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1z3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z3a OCA], [https://pdbe.org/1z3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1z3a RCSB], [https://www.ebi.ac.uk/pdbsum/1z3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1z3a ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1z3a TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/TADA_ECOLI TADA_ECOLI]] Deaminates adenosine-34 to inosine in tRNA-Arg2. Mutation in this protein makes E.coli resistant to the toxic proteins encoded by the gef gene family. Essential for cell viability.<ref>PMID:12110595</ref>
+[https://www.uniprot.org/uniprot/TADA_ECOLI TADA_ECOLI] Deaminates adenosine-34 to inosine in tRNA-Arg2. Mutation in this protein makes E.coli resistant to the toxic proteins encoded by the gef gene family. Essential for cell viability.<ref>PMID:12110595</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z3/1z3a_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z3/1z3a_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </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=1z3a ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The essential tRNA-specific adenosine deaminase catalyzes the deamination of adenosine to inosine at the wobble position of tRNAs. This modification allows for a single tRNA species to recognize multiple synonymous codons containing A, C, or U in the last (3'-most) position and ensures that all sense codons are appropriately decoded. We report the first combined structural and kinetic characterization of a wobble-specific deaminase. The structure of the Escherichia coli enzyme clearly defines the dimer interface and the coordination of the catalytically essential zinc ion. The structure also identifies the nucleophilic water and highlights residues near the catalytic zinc likely to be involved in recognition and catalysis of polymeric RNA substrates. A minimal 19 nucleotide RNA stem substrate has permitted the first steady-state kinetic characterization of this enzyme (k(cat) = 13 +/- 1 min(-)(1) and K(M) = 0.83 +/- 0.22 microM). A continuous coupled assay was developed to follow the reaction at high concentrations of polynucleotide substrates (&gt;10 microM). This work begins to define the chemical and structural determinants responsible for catalysis and substrate recognition and lays the foundation for detailed mechanistic analysis of this essential enzyme.
-Structural and kinetic characterization of Escherichia coli TadA, the wobble-specific tRNA deaminase.,Kim J, Malashkevich V, Roday S, Lisbin M, Schramm VL, Almo SC Biochemistry. 2006 May 23;45(20):6407-16. PMID:16700551<ref>PMID:16700551</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1z3a" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Adenosine deaminase|Adenosine deaminase]]
+*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Almo, S C]]
+[[Category: Large Structures]]
-[[Category: Burley, S K]]
+[[Category: Almo SC]]
-[[Category: Kim, J]]
+[[Category: Burley SK]]
-[[Category: Lisbin, M]]
+[[Category: Kim J]]
-[[Category: Malashkevich, V]]
+[[Category: Lisbin M]]
-[[Category: Structural genomic]]
+[[Category: Malashkevich V]]
-[[Category: Dimer]]
-[[Category: Hydrolase]]
-[[Category: Metalloenzyme]]
-[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Trna adenosine deaminase]]