3d6u: Difference between revisions

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==Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase==
The line below this paragraph, containing "STRUCTURE_3d6u", creates the "Structure Box" on the page.
<StructureSection load='3d6u' size='340' side='right'caption='[[3d6u]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3d6u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2q1g 2q1g]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D6U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D6U FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=T11:4-[3-(TRIFLUOROMETHYL)DIAZIRIDIN-3-YL]-L-PHENYLALANINE'>T11</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j1u|1j1u]], [[3d6v|3d6v]]</div></td></tr>
{{STRUCTURE_3d6u| PDB=3d6u |  SCENE= }}
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">tyrS, MJ0389 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </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=3d6u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d6u OCA], [https://pdbe.org/3d6u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d6u RCSB], [https://www.ebi.ac.uk/pdbsum/3d6u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d6u ProSAT]</span></td></tr>
</table>
== Function ==
[[https://www.uniprot.org/uniprot/SYY_METJA SYY_METJA]] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).<ref>PMID:10585437</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/d6/3d6u_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3d6u ConSurf].
<div style="clear:both"></div>


'''Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase'''
==See Also==
 
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 
== References ==
==About this Structure==
<references/>
3D6U is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2q1g 2q1g]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D6U OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Atcc 43067]]
A genetically encoded diazirine photocrosslinker in Escherichia coli., Tippmann EM, Liu W, Summerer D, Mack AV, Schultz PG, Chembiochem. 2007 Dec 17;8(18):2210-4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18000916 18000916]
[[Category: Large Structures]]
[[Category: Methanocaldococcus jannaschii]]
[[Category: Single protein]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Tyrosine--tRNA ligase]]
[[Category: Liu, W.]]
[[Category: Liu, W]]
[[Category: Mack, A V.]]
[[Category: Mack, A V]]
[[Category: Schultz, P G.]]
[[Category: Schultz, P G]]
[[Category: Tippmann, E.]]
[[Category: Tippmann, E]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Aminoacyl-trna synthetase]]
[[Category: Atp-binding]]
[[Category: Atp-binding]]
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[[Category: Photocrosslinking unnatural amino acid]]
[[Category: Photocrosslinking unnatural amino acid]]
[[Category: Protein biosynthesis]]
[[Category: Protein biosynthesis]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 28 09:26:28 2008''

Latest revision as of 22:20, 20 October 2021

Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetaseCrystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase

Structural highlights

3d6u is a 1 chain structure with sequence from Atcc 43067. This structure supersedes the now removed PDB entry 2q1g. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Gene:tyrS, MJ0389 (ATCC 43067)
Activity:Tyrosine--tRNA ligase, with EC number 6.1.1.1
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[SYY_METJA] Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr-AMP and then transferred to the acceptor end of tRNA(Tyr).[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Steer BA, Schimmel P. Major anticodon-binding region missing from an archaebacterial tRNA synthetase. J Biol Chem. 1999 Dec 10;274(50):35601-6. PMID:10585437

3d6u, resolution 2.20Å

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