1e22: Difference between revisions

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-{{Seed}}
-[[Image:1e22.png|left|200px]]
-<!--
+==LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and the non-hydrolysable atp analogue amp-pcp==
-The line below this paragraph, containing "STRUCTURE_1e22", creates the "Structure Box" on the page.
+<StructureSection load='1e22' size='340' side='right'caption='[[1e22]], [[Resolution|resolution]] 2.43&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'>[[1e22]] 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=1E22 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E22 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-{{STRUCTURE_1e22|  PDB=1e22  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e22 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e22 OCA], [https://pdbe.org/1e22 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e22 RCSB], [https://www.ebi.ac.uk/pdbsum/1e22 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e22 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYK2_ECOLI SYK2_ECOLI] Also can synthesize a number of adenyl dinucleotides (in particular AppppA). These dinucleotides have been proposed to act as modulators of the heat-shock response and stress response.[HAMAP-Rule:MF_00252]
+== 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/e2/1e22_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=1e22 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aminoacyl-tRNA synthetases play a key role in protein biosynthesis by catalyzing the specific aminoacylation of tRNA. The energy required for the formation of the ester bond between the amino acid carboxylate group and the tRNA acceptor stem is supplied by coupling the reaction to the hydrolysis of ATP. Lysyl-tRNA synthetase from Escherichia coli belongs to the family of class II synthetases and carries out a two-step reaction, in which lysine is activated by being attached to the alpha-phosphate of AMP before being transferred to the cognate tRNA. Crystals of the thermo-inducible E. coli lysyl-tRNA synthetase LysU which diffract to 2.1 A resolution have been used to determine crystal structures of the enzyme in the presence of lysine, the lysyl-adenylate intermediate, and the nonhydrolyzable ATP analogue AMP-PCP. Additional data have been obtained from crystals soaked in a solution containing ATP and Mn(2+). The refined crystal structures give "snapshots" of the active site corresponding to key steps in the aminoacylation reaction and provide the structural framework for understanding the mechanism of lysine activation. The active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilize the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding.
-===LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH LYSINE AND THE NON-HYDROLYSABLE ATP ANALOGUE AMP-PCP===
+Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction.,Desogus G, Todone F, Brick P, Onesti S Biochemistry. 2000 Jul 25;39(29):8418-25. PMID:10913247<ref>PMID:10913247</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e22" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10913247}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10913247 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10913247}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-E22 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E22 OCA].
+[[Category: Large Structures]]
+[[Category: Brick P]]
-==Reference==
+[[Category: Desogus G]]
-Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction., Desogus G, Todone F, Brick P, Onesti S, Biochemistry. 2000 Jul 25;39(29):8418-25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10913247 10913247]
+[[Category: Onesti S]]
-[[Category: Escherichia coli]]
+[[Category: Todone F]]
-[[Category: Lysine--tRNA ligase]]
-[[Category: Single protein]]
-[[Category: Brick, P.]]
-[[Category: Desogus, G.]]
-[[Category: Onesti, S.]]
-[[Category: Todone, F.]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Ligase]]
-[[Category: Protein biosynthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 00:00:53 2008''