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1bbu

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(New page: 200px<br /><applet load="1bbu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bbu, resolution 2.7&Aring;" /> '''LYSYL-TRNA SYNTHETASE...)
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[[Image:1bbu.gif|left|200px]]<br /><applet load="1bbu" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bbu, resolution 2.7&Aring;" />
 
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'''LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE'''<br />
 
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==Overview==
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==LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE==
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Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA, synthetases and catalyses the specific aminoacylation of tRNA(Lys). The, crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from, Escherichia coli has been determined to 2.7 A resolution in the unliganded, form and in a complex with the lysine substrate. A comparison between the, unliganded and lysine-bound structures reveals major conformational, changes upon lysine binding. The lysine substrate is involved in a network, of hydrogen bonds. Two of these interactions, one between the alpha-amino, group and the carbonyl oxygen of Gly 216 and the other between the, carboxylate group and the side chain of Arg 262, trigger a subtle and, complicated reorganization of the active site, involving the ordering of, two loops (residues 215-217 and 444-455), a change in conformation of, residues 393-409, and a rotation of a 4-helix bundle domain (located, between motif 2 and 3) by 10 degrees. The result of these changes is a, closing up of the active site upon lysine binding.
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<StructureSection load='1bbu' size='340' side='right'caption='[[1bbu]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bbu]] is a 1 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=1BBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BBU 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]] 2.7&#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=LYS:LYSINE'>LYS</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=1bbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bbu OCA], [https://pdbe.org/1bbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bbu RCSB], [https://www.ebi.ac.uk/pdbsum/1bbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bbu ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYK1_ECOLI SYK1_ECOLI]
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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/bb/1bbu_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=1bbu ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNA(Lys). The crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli has been determined to 2.7 A resolution in the unliganded form and in a complex with the lysine substrate. A comparison between the unliganded and lysine-bound structures reveals major conformational changes upon lysine binding. The lysine substrate is involved in a network of hydrogen bonds. Two of these interactions, one between the alpha-amino group and the carbonyl oxygen of Gly 216 and the other between the carboxylate group and the side chain of Arg 262, trigger a subtle and complicated reorganization of the active site, involving the ordering of two loops (residues 215-217 and 444-455), a change in conformation of residues 393-409, and a rotation of a 4-helix bundle domain (located between motif 2 and 3) by 10 degrees. The result of these changes is a closing up of the active site upon lysine binding.
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==About this Structure==
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Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.,Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P Biochemistry. 2000 Oct 24;39(42):12853-61. PMID:11041850<ref>PMID:11041850</ref>
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1BBU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with LYS as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Lysine--tRNA_ligase Lysine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.6 6.1.1.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1BBU OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding., Onesti S, Desogus G, Brevet A, Chen J, Plateau P, Blanquet S, Brick P, Biochemistry. 2000 Oct 24;39(42):12853-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11041850 11041850]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1bbu" style="background-color:#fffaf0;"></div>
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[[Category: Lysine--tRNA ligase]]
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[[Category: Single protein]]
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[[Category: Blanquet, S.]]
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[[Category: Brevet, A.]]
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[[Category: Brick, P.]]
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[[Category: Chen, J.]]
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[[Category: Desogus, G.]]
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[[Category: Onesti, S.]]
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[[Category: Plateau, P.]]
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[[Category: LYS]]
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[[Category: aminoacyl-trna synthetase]]
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[[Category: ligase]]
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[[Category: protein biosynthesis]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 11:31:42 2007''
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==See Also==
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Escherichia coli K-12]]
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[[Category: Large Structures]]
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[[Category: Blanquet S]]
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[[Category: Brevet A]]
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[[Category: Brick P]]
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[[Category: Chen J]]
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[[Category: Desogus G]]
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[[Category: Onesti S]]
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[[Category: Plateau P]]

Current revision

LYSYL-TRNA SYNTHETASE (LYSS) COMPLEXED WITH LYSINE

PDB ID 1bbu

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