1n3l

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[[Image:1n3l.jpg|left|200px]]<br /><applet load="1n3l" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1n3l, resolution 1.18&Aring;" />
 
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'''Crystal structure of a human aminoacyl-tRNA synthetase cytokine'''<br />
 
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==Overview==
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==Crystal structure of a human aminoacyl-tRNA synthetase cytokine==
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The 20 aminoacyl-tRNA synthetases catalyze the first step of protein, synthesis and establish the rules of the genetic code through, aminoacylation reactions. Biological fragments of two human enzymes, tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase, connect, protein synthesis to cell-signaling pathways including angiogenesis., Alternative splicing or proteolysis produces these fragments. The, proangiogenic N-terminal fragment mini-TyrRS has IL-8-like cytokine, activity that, like other CXC cytokines, depends on a Glu-Leu-Arg motif., Point mutations in this motif abolish cytokine activity. The full-length, native TyrRS lacks cytokine activity. No structure has been available for, any mammalian tRNA synthetase that, in turn, might give insight into why, mini-TyrRS and not TyrRS has cytokine activities. Here, the structure of, human mini-TyrRS, which contains both the catalytic and the anticodon, recognition domain, is reported to a resolution of 1.18 A. The critical, Glu-Leu-Arg motif is located on an internal alpha-helix of the catalytic, domain, where the guanidino side chain of R is part of a hydrogen-bonding, network tethering the anticodon-recognition domain back to the catalytic, site. Whereas the catalytic domains of the human and bacterial enzymes, superimpose, the spatial disposition of the anticodon recognition domain, relative to the catalytic domain is unique in mini-TyrRS relative to the, bacterial orthologs. This unique orientation of the anticodon-recognition, domain can explain why the fragment mini-TyrRS, and not full-length native, TyrRS, is active in cytokine-signaling pathways.
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<StructureSection load='1n3l' size='340' side='right'caption='[[1n3l]], [[Resolution|resolution]] 1.18&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1n3l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N3L FirstGlance]. <br>
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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]] 1.18&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=1n3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n3l OCA], [https://pdbe.org/1n3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n3l RCSB], [https://www.ebi.ac.uk/pdbsum/1n3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n3l ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/SYYC_HUMAN SYYC_HUMAN] Defects in YARS are the cause of Charcot-Marie-Tooth disease dominant intermediate type C (CMTDIC) [MIM:[https://omim.org/entry/608323 608323]. CMTDIC is a form of Charcot-Marie-Tooth disease characterized by clinical and pathologic features intermediate between demyelinating and axonal peripheral neuropathies, and motor median nerve conduction velocities ranging from 25 to 45 m/sec.<ref>PMID:16429158</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/SYYC_HUMAN SYYC_HUMAN] 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) (By similarity).
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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/n3/1n3l_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=1n3l ConSurf].
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<div style="clear:both"></div>
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==Disease==
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==See Also==
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Known disease associated with this structure: Charcot-Marie-Tooth disease, dominant intermediate C OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603623 603623]]
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1N3L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N3L OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Crystal structure of a human aminoacyl-tRNA synthetase cytokine., Yang XL, Skene RJ, McRee DE, Schimmel P, Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15369-74. Epub 2002 Nov 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12427973 12427973]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Tyrosine--tRNA ligase]]
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[[Category: McRee DE]]
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[[Category: McRee, D.E.]]
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[[Category: Schimmel P]]
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[[Category: Schimmel, P.]]
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[[Category: Skene RJ]]
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[[Category: Skene, R.J.]]
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[[Category: Yang X-L]]
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[[Category: Yang, X.L.]]
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[[Category: GOL]]
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[[Category: SO4]]
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[[Category: dimer]]
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[[Category: rossmann fold as catalytic domain]]
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[[Category: unique anticodon recognition domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 16:26:54 2008''
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Current revision

Crystal structure of a human aminoacyl-tRNA synthetase cytokine

PDB ID 1n3l

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