1j8b

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(New page: 200px<br /><applet load="1j8b" size="450" color="white" frame="true" align="right" spinBox="true" caption="1j8b, resolution 1.75&Aring;" /> '''Structure of YbaB fr...)
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[[Image:1j8b.gif|left|200px]]<br /><applet load="1j8b" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1j8b, resolution 1.75&Aring;" />
 
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'''Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function'''<br />
 
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==Overview==
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==Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function==
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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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<StructureSection load='1j8b' size='340' side='right'caption='[[1j8b]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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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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1J8B is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J8B OCA].
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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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==Reference==
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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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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12571243 12571243]
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</table>
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[[Category: Haemophilus influenzae]]
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== Function ==
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[[Category: Single protein]]
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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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[[Category: Eisenstein, E.]]
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== Evolutionary Conservation ==
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[[Category: Herzberg, O.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Howard, A.]]
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Check<jmol>
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[[Category: Lim, K.]]
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<jmolCheckbox>
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[[Category: Parsons, J.F.]]
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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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[[Category: S2F, Structure.2.Function.Project.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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[[Category: Tempcyzk, A.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: Toedt, J.]]
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</jmolCheckbox>
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[[Category: hi0442]]
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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: hypothetical protein]]
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<div style="clear:both"></div>
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[[Category: s2f]]
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__TOC__
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[[Category: structural genomics]]
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</StructureSection>
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[[Category: structure 2 function project]]
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[[Category: Haemophilus influenzae Rd KW20]]
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[[Category: Large Structures]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:00:30 2007''
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[[Category: Eisenstein E]]
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[[Category: Herzberg O]]
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[[Category: Howard A]]
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[[Category: Lim K]]
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[[Category: Parsons JF]]
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[[Category: Tempcyzk A]]
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[[Category: Toedt J]]

Current revision

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

PDB ID 1j8b

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