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| - | [[Image:2ov4.jpg|left|200px]]<br /><applet load="2ov4" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="2ov4, resolution 2.50Å" /> | |
| - | '''Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with adenosine tetraphosphate'''<br /> | |
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| - | ==Overview== | + | ==Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with adenosine tetraphosphate== |
| - | Tryptophanyl-tRNA synthetase (TrpRS) is a functionally dimeric ligase, which specifically couples hydrolysis of ATP to AMP and pyrophosphate to, the formation of an ester bond between tryptophan and the cognate tRNA., TrpRS from Bacillus stearothermophilus binds the ATP analogue, adenosine-5' tetraphosphate (AQP) competitively with ATP during, pyrophosphate exchange. Estimates of binding affinity from this, competitive inhibition and from isothermal titration calorimetry show that, AQP binds 200 times more tightly than ATP both under conditions of, induced-fit, where binding is coupled to an unfavorable conformational, change, and under exchange conditions, where there is no conformational, change. These binding data provide an indirect experimental measurement of, +3.0 kcal/mol for the conformational free energy change associated with, induced-fit assembly of the active site. Thermodynamic parameters derived, from the calorimetry reveal very modest enthalpic changes, consistent with, binding driven largely by a favorable entropy change. The 2.5 A structure, of the TrpRS:AQP complex, determined de novo by X-ray crystallography, resembles that of the previously described, pre-transition state TrpRS:ATP, complexes. The anticodon-binding domain untwists relative to the, Rossmann-fold domain by 20% of the way toward the orientation observed for, the Products complex. An unexpected tetraphosphate conformation allows the, gamma and deltad phosphate groups to occupy positions equivalent to those, occupied by the beta and gamma phosphates of ATP. The beta-phosphate, effects a 1.11 A extension that relocates the alpha-phosphate toward the, tryptophan carboxylate while the PPi mimic moves deeper into the KMSKS, loop. This configuration improves interactions between enzyme and, nucleotide significantly and uniformly in the adenosine and PPi binding, subsites. A new hydrogen bond forms between S194 from the class I KMSKS, signature sequence and the PPi mimic. These complementary thermodynamic, and structural data are all consistent with the conclusion that the, tetraphosphate mimics a transition-state in which the KMSKS loop develops, increasingly tight bonds to the PPi leaving group, weakening linkage to, the Palpha as it is relocated by an energetically favorable domain, movement. Consistent with extensive mutational data on Tyrosyl-tRNA, synthetase, this aspect of the mechanism develops high transition-state, affinity for the adenosine and pyrophosphate moieties, which move, significantly, relative to one another, during the catalytic step.
| + | <StructureSection load='2ov4' size='340' side='right'caption='[[2ov4]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[2ov4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OV4 FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANL:ANILINE'>ANL</scene>, <scene name='pdbligand=AQP:ADENOSINE-5-TETRAPHOSPHATE'>AQP</scene>, <scene name='pdbligand=CS:CESIUM+ION'>CS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=2ov4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ov4 OCA], [https://pdbe.org/2ov4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ov4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ov4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ov4 ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/SYW_GEOSE SYW_GEOSE] |
| | + | == 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/ov/2ov4_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=2ov4 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 2OV4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus] with <scene name='pdbligand=CS:'>CS</scene>, <scene name='pdbligand=AQP:'>AQP</scene>, <scene name='pdbligand=ANL:'>ANL</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Tryptophan--tRNA_ligase Tryptophan--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.2 6.1.1.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OV4 OCA].
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Reference==
| + | </StructureSection> |
| - | Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Adenosine-5' Tetraphosphate: Evidence for Distributed Use of Catalytic Binding Energy in Amino Acid Activation by Class I Aminoacyl-tRNA Synthetases., Retailleau P, Weinreb V, Hu M, Carter CW Jr, J Mol Biol. 2007 May 25;369(1):108-28. Epub 2007 Mar 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17428498 17428498]
| + | |
| | [[Category: Geobacillus stearothermophilus]] | | [[Category: Geobacillus stearothermophilus]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Tryptophan--tRNA ligase]]
| + | [[Category: Carter Jr CW]] |
| - | [[Category: Jr., C.W.Carter.]] | + | [[Category: Retailleau P]] |
| - | [[Category: Retailleau, P.]] | + | |
| - | [[Category: ANL]]
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| - | [[Category: AQP]]
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| - | [[Category: CS]]
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| - | [[Category: GOL]]
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| - | [[Category: aminoacyl-trna synthetase]]
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| - | [[Category: nucleotide binding site]]
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| - | [[Category: rossmann fold]]
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| - | [[Category: transition state analog inhibitor]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:09:42 2008''
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