|
|
| (17 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| [[Image:1d2r.jpg|left|200px]]<br /><applet load="1d2r" size="450" color="white" frame="true" align="right" spinBox="true"
| |
| caption="1d2r, resolution 2.90Å" />
| |
| '''2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.'''<br />
| |
|
| |
|
| ==Overview== | | ==2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.== |
| The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS), was solved at 2.9 A using a combination of molecular replacement and, maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP, complex (TAM; Doublie S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray, scattering experiments, unliganded TrpRS has a conformation in which both, monomers open, leaving only the tryptophan-binding regions of their active, sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature, sequences, and the distal helical domain rotate as a single rigid body, away from the dinucleotide-binding fold domain, opening the AMP binding, site, seen in the TAM complex, into two halves. Comparison of side-chain, packing in ligand-free TrpRS and the TAM complex, using identification of, nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that, significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain, rearrangements provide a new structural paradigm that is consistent in, detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et, al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry, 27:1581-1587). Coupling of ATP binding determinants associated with the, two catalytic signature sequences to the helical domain containing the, presumptive anticodon-binding site provides a mechanism to coordinate, active-site chemistry with relocation of the major tRNA binding, determinants.
| | <StructureSection load='1d2r' size='340' side='right'caption='[[1d2r]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == |
| | <table><tr><td colspan='2'>[[1d2r]] is a 6 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=1D2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D2R 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]] 2.9Å</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=1d2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d2r OCA], [https://pdbe.org/1d2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d2r RCSB], [https://www.ebi.ac.uk/pdbsum/1d2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d2r 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/d2/1d2r_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=1d2r ConSurf]. |
| | <div style="clear:both"></div> |
|
| |
|
| ==About this Structure== | | ==See Also== |
| 1D2R is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D2R OCA].
| | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | | __TOC__ |
| ==Reference==
| | </StructureSection> |
| 2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site., Ilyin VA, Temple B, Hu M, Li G, Yin Y, Vachette P, Carter CW Jr, Protein Sci. 2000 Feb;9(2):218-31. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10716174 10716174]
| |
| [[Category: Geobacillus stearothermophilus]] | | [[Category: Geobacillus stearothermophilus]] |
| [[Category: Single protein]] | | [[Category: Large Structures]] |
| [[Category: Tryptophan--tRNA ligase]] | | [[Category: Carter Jr CW]] |
| [[Category: Ilyin, V.A.]] | | [[Category: Ilyin VA]] |
| [[Category: Jr., C.W.Carter.]]
| |
| [[Category: aars]]
| |
| [[Category: class i trna synthetase]]
| |
| [[Category: induced fit]]
| |
| [[Category: trprs]]
| |
| | |
| ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:58:33 2007''
| |
