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1j8b

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[[Image:1j8b.gif|left|200px]]
 
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==Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function==
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The line below this paragraph, containing "STRUCTURE_1j8b", creates the "Structure Box" on the page.
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<StructureSection load='1j8b' size='340' side='right'caption='[[1j8b]], [[Resolution|resolution]] 1.75&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'>[[1j8b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J8B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J8B 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]] 1.75&#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></td></tr>
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{{STRUCTURE_1j8b| PDB=1j8b | 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=1j8b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j8b OCA], [https://pdbe.org/1j8b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j8b RCSB], [https://www.ebi.ac.uk/pdbsum/1j8b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j8b ProSAT]</span></td></tr>
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</table>
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'''Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function'''
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== Function ==
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[https://www.uniprot.org/uniprot/Y442_HAEIN Y442_HAEIN] Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection (By similarity).[HAMAP-Rule:MF_00274]
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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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D-Tyr-tRNA(Tyr) deacylase is an editing enzyme that removes d-tyrosine and other d-amino acids from charged tRNAs, thereby preventing incorrect incorporation of d-amino acids into proteins. A model for the catalytic mechanism of this enzyme is proposed based on the crystal structure of the enzyme from Haemophilus influenzae determined at a 1.64-A resolution. Structural comparison of this dimeric enzyme with the very similar structure of the enzyme from Escherichia coli together with sequence analyses indicate that the active site is located in the dimer interface within a depression that includes an invariant threonine residue, Thr-80. The active site contains an oxyanion hole formed by the main chain nitrogen atoms of Thr-80 and Phe-79 and the side chain amide group of the invariant Gln-78. The Michaelis complex between the enzyme and D-Tyr-tRNA was modeled assuming a nucleophilic attack on the carbonyl carbon of D-Tyr by the Thr-80 O(gamma) atom and a role for the oxyanion hole in stabilizing the negatively charged tetrahedral transition states. The model is consistent with all of the available data on substrate specificity. Based on this model, we propose a substrate-assisted acylation/deacylation-catalytic mechanism in which the amino group of the D-Tyr is deprotonated and serves as the general base.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j8/1j8b_consurf.spt"</scriptWhenChecked>
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1J8B is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J8B OCA].
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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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==Reference==
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</jmolCheckbox>
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A catalytic mechanism for D-Tyr-tRNATyr deacylase based on the crystal structure of Hemophilus influenzae HI0670., Lim K, Tempczyk A, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O, J Biol Chem. 2003 Apr 11;278(15):13496-502. Epub 2003 Feb 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12571243 12571243]
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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=1j8b ConSurf].
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[[Category: Haemophilus influenzae]]
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<div style="clear:both"></div>
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[[Category: Single protein]]
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__TOC__
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[[Category: Eisenstein, E.]]
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</StructureSection>
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[[Category: Herzberg, O.]]
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[[Category: Haemophilus influenzae Rd KW20]]
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[[Category: Howard, A.]]
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[[Category: Large Structures]]
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[[Category: Lim, K.]]
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[[Category: Eisenstein E]]
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[[Category: Parsons, J F.]]
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[[Category: Herzberg O]]
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[[Category: S2F, Structure 2.Function Project.]]
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[[Category: Howard A]]
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[[Category: Tempcyzk, A.]]
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[[Category: Lim K]]
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[[Category: Toedt, J.]]
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[[Category: Parsons JF]]
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[[Category: Hi0442]]
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[[Category: Tempcyzk A]]
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[[Category: Hypothetical protein]]
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[[Category: Toedt J]]
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[[Category: S2f]]
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[[Category: Structural genomic]]
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[[Category: Structure 2 function project]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:54:37 2008''
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Current revision

Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function

PDB ID 1j8b

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