1dbu

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[[Image:1dbu.jpg|left|200px]]<br /><applet load="1dbu" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dbu, resolution 1.8&Aring;" />
 
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'''Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)'''<br />
 
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==Overview==
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==Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)==
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Structural genomics of proteins of unknown function most straightforwardly assists with assignment of biochemical activity when the new structure resembles that of proteins whose functions are known. When a new fold is revealed, the universe of known folds is enriched, and once the function is determined by other means, novel structure-function relationships are established. The previously unannotated protein HI1434 from H. influenzae provides a hybrid example of these two paradigms. It is a member of a microbial protein family, labeled in SwissProt as YbaK and ebsC. The crystal structure at 1.8 A resolution reported here reveals a fold that is only remotely related to the C-lectin fold, in particular to endostatin, and thus is not sufficiently similar to imply that YbaK proteins are saccharide binding proteins. However, a crevice that may accommodate a small ligand is evident. The putative binding site contains only one invariant residue, Lys46, which carries a functional group that could play a role in catalysis, indicating that YbaK is probably not an enzyme. Detailed sequence analysis, including a number of newly sequenced microbial organisms, highlights sequence homology to an insertion domain in prolyl-tRNA synthetases (proRS) from prokaryote, a domain whose function is unknown. A HI1434-based model of the insertion domain shows that it should also contain the putative binding site. Being part of a tRNA synthetases, the insertion domain is likely to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. By analogy, YbaK may also play a role in nucleotide or oligonucleotide binding, the nature of which is yet to be determined.
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<StructureSection load='1dbu' size='340' side='right'caption='[[1dbu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dbu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBU FirstGlance]. <br>
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1DBU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with <scene name='pdbligand=HG:'>HG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBU 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]] 1.8&#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=HG:MERCURY+(II)+ION'>HG</scene>, <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=1dbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbu OCA], [https://pdbe.org/1dbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbu RCSB], [https://www.ebi.ac.uk/pdbsum/1dbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbu ProSAT]</span></td></tr>
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Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications., Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O, Proteins. 2000 Jul 1;40(1):86-97. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10813833 10813833]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/YBAK_HAEIN YBAK_HAEIN] Functions in trans to edit the amino acid from incorrectly charged Cys-tRNA(Pro) via a Cys-tRNA(Pro) deacylase activity. Probably compensates for the lack of Cys-tRNA(Pro) editing by ProRS. Is also able to deacylate Cys-tRNA(Cys), and displays weak deacylase activity in vitro against Gly-tRNA(Gly), as well as, at higher concentrations, some other correctly charged tRNAs. Does not cleave Pro-tRNA(Pro).<ref>PMID:15322138</ref> <ref>PMID:15886196</ref> <ref>PMID:21768119</ref>
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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/db/1dbu_consurf.spt"</scriptWhenChecked>
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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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</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=1dbu ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Herzberg, O.]]
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[[Category: Herzberg O]]
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[[Category: Huang, K.]]
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[[Category: Huang K]]
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[[Category: Li, Z.]]
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[[Category: Li Z]]
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[[Category: S2F, Structure 2.Function Project.]]
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[[Category: Zhang H]]
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[[Category: Zhang, H.]]
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[[Category: HG]]
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[[Category: s2f]]
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[[Category: structural genomics]]
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[[Category: structure 2 function project]]
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[[Category: ybak]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:15:05 2008''
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Current revision

Crystal structure of cysteinyl-tRNA(Pro) deacylase protein from H. influenzae (HI1434)

PDB ID 1dbu

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