1okj
From Proteopedia
(Difference between revisions)
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<StructureSection load='1okj' size='340' side='right'caption='[[1okj]], [[Resolution|resolution]] 2.28Å' scene=''> | <StructureSection load='1okj' size='340' side='right'caption='[[1okj]], [[Resolution|resolution]] 2.28Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1okj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1okj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OKJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</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]] 2.28Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GD3:GADOLINIUM+ION'>GD3</scene></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=1okj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okj OCA], [https://pdbe.org/1okj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1okj RCSB], [https://www.ebi.ac.uk/pdbsum/1okj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1okj ProSAT], [https://www.topsan.org/Proteins/BIGS/1okj 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=1okj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1okj OCA], [https://pdbe.org/1okj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1okj RCSB], [https://www.ebi.ac.uk/pdbsum/1okj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1okj ProSAT], [https://www.topsan.org/Proteins/BIGS/1okj TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/TSAB_ECOLI TSAB_ECOLI] Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. In fact, can act as a protease that specifically degrades TsaD in vitro; therefore TsaB may post-translationally regulate cellular pools of TsaD via proteolytic degradation. Does not show sialoglycoprotease activity against glycophorin A.<ref>PMID:19376873</ref> <ref>PMID:22378793</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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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=1okj ConSurf]. | </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=1okj ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | A set of seven caged gadolinium complexes were used as vectors for introducing the chelated Gd(3+) ion into protein crystals in order to provide strong anomalous scattering for de novo phasing. The complexes contained multidentate ligand molecules with different functional groups to provide a panel of possible interactions with the protein. An exhaustive crystallographic analysis showed them to be nondisruptive to the diffraction quality of the prepared derivative crystals, and as many as 50% of the derivatives allowed the determination of accurate phases, leading to high-quality experimental electron-density maps. At least two successful derivatives were identified for all tested proteins. Structure refinement showed that the complexes bind to the protein surface or solvent-accessible cavities, involving hydrogen bonds, electrostatic and CH-pi interactions, explaining their versatile binding modes. Their high phasing power, complementary binding modes and ease of use make them highly suitable as a heavy-atom screen for high-throughput de novo structure determination, in combination with the SAD method. They can also provide a reliable tool for the development of new methods such as serial femtosecond crystallography. | ||
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| - | A complement to the modern crystallographer's toolbox: caged gadolinium complexes with versatile binding modes.,Stelter M, Molina R, Jeudy S, Kahn R, Abergel C, Hermoso JA Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1506-16. doi:, 10.1107/S1399004714005483. Epub 2014 May 23. PMID:24914962<ref>PMID:24914962</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1okj" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Escherichia coli K-12]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Abergel | + | [[Category: Abergel C]] |
| - | [[Category: Claverie | + | [[Category: Claverie JM]] |
| - | [[Category: Jeudy | + | [[Category: Jeudy S]] |
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Revision as of 05:48, 17 April 2024
crystal structure of the essential E. coli YeaZ protein by MAD method using the gadolinium complex "DOTMA"
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