1dbx: Difference between revisions

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{{Seed}}
[[Image:1dbx.png|left|200px]]


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==Crystal structure of cysteinyl-tRNA(Pro) deacylase from H. influenzae (HI1434)==
The line below this paragraph, containing "STRUCTURE_1dbx", creates the "Structure Box" on the page.
<StructureSection load='1dbx' size='340' side='right'caption='[[1dbx]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dbx]] is a 2 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=1DBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBX FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_1dbx|  PDB=1dbx  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbx OCA], [https://pdbe.org/1dbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbx RCSB], [https://www.ebi.ac.uk/pdbsum/1dbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbx ProSAT]</span></td></tr>
</table>
== Function ==
[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>
== 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/db/1dbx_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1dbx ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===Crystal structure of cysteinyl-tRNA(Pro) deacylase from H. influenzae (HI1434)===
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:10813833<ref>PMID:10813833</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 10813833 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_10813833}}
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</StructureSection>
==About this Structure==
1DBX 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=1DBX OCA].
 
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/10813833 10813833]
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Herzberg, O.]]
[[Category: Herzberg O]]
[[Category: Huang, K.]]
[[Category: Huang K]]
[[Category: Li, Z.]]
[[Category: Li Z]]
[[Category: S2F, Structure 2.Function Project.]]
[[Category: Zhang H]]
[[Category: Zhang, H.]]
[[Category: S2f]]
[[Category: Structural genomic]]
[[Category: Structure 2 function project]]
[[Category: Ybak]]
 
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Retrieved from "https://proteopedia.org/1dbx"