1kmn

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[[Image:1kmn.gif|left|200px]]<br /><applet load="1kmn" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kmn, resolution 2.8&Aring;" />
 
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'''HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP'''<br />
 
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==Overview==
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==HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP==
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The crystal structure of an enzyme-substrate complex with histidyl-tRNA, synthetase from Escherichia coli, ATP, and the amino acid analog, histidinol is described and compared with the previously obtained, enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the, catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is, substituted with histidine, the apparent second order rate constant, (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation, reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked, with MnCl2 reveal the existence of two metal binding sites between beta-, and gamma-phosphates; these sites appear to stabilize the conformation of, the pyrophosphate. The use of both conserved metal ions and arginine in, phosphoryl transfer provides evidence of significant early functional, divergence of class II aminoacyl-tRNA synthetases.
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<StructureSection load='1kmn' size='340' side='right'caption='[[1kmn]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kmn]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KMN 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]] 2.8&#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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=HSO:L-HISTIDINOL'>HSO</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=1kmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kmn OCA], [https://pdbe.org/1kmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kmn RCSB], [https://www.ebi.ac.uk/pdbsum/1kmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kmn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYH_ECOLI SYH_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/km/1kmn_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=1kmn 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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The crystal structure of an enzyme-substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl2 reveal the existence of two metal binding sites between beta- and gamma-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.
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==About this Structure==
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The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase.,Arnez JG, Augustine JG, Moras D, Francklyn CS Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7144-9. PMID:9207058<ref>PMID:9207058</ref>
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1KMN 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 <scene name='pdbligand=HSO:'>HSO</scene> and <scene name='pdbligand=ATP:'>ATP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Histidine--tRNA_ligase Histidine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.21 6.1.1.21] Known structural/functional Sites: <scene name='pdbsite=S1A:HIS+And+Atp+Binding+Site,+Substrates+Of+First+Reaction+H+...'>S1A</scene>, <scene name='pdbsite=S1B:HIS+And+Atp+Binding+Site,+Substrates+Of+First+Reaction+H+...'>S1B</scene>, <scene name='pdbsite=S1C:HIS+And+Atp+Binding+Site,+Substrates+Of+First+Reaction+H+...'>S1C</scene> and <scene name='pdbsite=S1D:HIS+And+Atp+Binding+Site,+Substrates+Of+First+Reaction+H+...'>S1D</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KMN 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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The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase., Arnez JG, Augustine JG, Moras D, Francklyn CS, Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7144-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9207058 9207058]
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</div>
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[[Category: Escherichia coli]]
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<div class="pdbe-citations 1kmn" style="background-color:#fffaf0;"></div>
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[[Category: Histidine--tRNA ligase]]
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[[Category: Single protein]]
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[[Category: Arnez, J.G.]]
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[[Category: Francklyn, C.S.]]
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[[Category: Moras, D.]]
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[[Category: ATP]]
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[[Category: HSO]]
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[[Category: aminoacyl-trna synthase]]
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[[Category: ligase]]
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[[Category: synthetase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:52:56 2008''
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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]]
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[[Category: Large Structures]]
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[[Category: Arnez JG]]
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[[Category: Francklyn CS]]
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[[Category: Moras D]]

Current revision

HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDINOL AND ATP

PDB ID 1kmn

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