1mb2: Difference between revisions

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New page: left|200px<br /><applet load="1mb2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mb2, resolution 2.7Å" /> '''Crystal Structure of ...
 
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[[Image:1mb2.jpg|left|200px]]<br /><applet load="1mb2" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1mb2, resolution 2.7&Aring;" />
'''Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation'''<br />


==Overview==
==Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation==
Binding ATP to tryptophanyl-tRNA synthetase (TrpRS) in a catalytically, competent configuration for amino acid activation destabilizes the enzyme, structure prior to forming the transition state. This conclusion follows, from monitoring the titration of TrpRS with ATP by small angle solution, X-ray scattering, enzyme activity, and crystal structures. ATP induces a, significantly smaller radius of gyration at pH=7 with a transition, midpoint at approximately 8mM. A non-reciprocal dependence of Trp and ATP, dissociation constants on concentrations of the second substrate show that, Trp binding enhances affinity for ATP, while the affinity for Trp falls, with the square of the [ATP] over the same concentration range (, approximately 5mM) that induces the more compact conformation. Two, distinct TrpRS:ATP structures have been solved, a high-affinity complex, grown with 1mM ATP and a low-affinity complex grown at 10mM ATP. The, former is isomorphous with unliganded TrpRS and the Trp complex from, monoclinic crystals. Reacting groups of the two individually-bound, substrates are separated by 6.7A. Although it lacks tryptophan, the, low-affinity complex has a closed conformation similar to that observed in, the presence of both ATP and Trp analogs such as indolmycin, and resembles, a complex previously postulated to form in the closely-related TyrRS upon, induced-fit active-site assembly, just prior to catalysis. Titration of, TrpRS with ATP therefore successively produces structurally distinct high-, and low-affinity ATP-bound states. The higher quality X-ray data for the, closed ATP complex (2.2A) provide new structural details likely related to, catalysis, including an extension of the KMSKS loop that engages the, second lysine and serine residues, K195 and S196, with the alpha and, gamma-phosphates; interactions of the K111 side-chain with the, gamma-phosphate; and a water molecule bridging the consensus sequence, residue T15 to the beta-phosphate. Induced-fit therefore strengthens, active-site interactions with ATP, substantially intensifying the, interaction of the KMSKS loop with the leaving PP(i) group. Formation of, this conformation in the absence of a Trp analog implies that ATP is a key, allosteric effector for TrpRS. The paradoxical requirement for high [ATP], implies that Gibbs binding free energy is stored in an unfavorable protein, conformation and can then be recovered for useful purposes, including, catalysis in the case of TrpRS.
<StructureSection load='1mb2' size='340' side='right'caption='[[1mb2]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1mb2]] 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=1MB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MB2 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]] 2.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</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=1mb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mb2 OCA], [https://pdbe.org/1mb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mb2 RCSB], [https://www.ebi.ac.uk/pdbsum/1mb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mb2 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/mb/1mb2_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=1mb2 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1MB2 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 TRP as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1MB2 OCA].
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations., Retailleau P, Huang X, Yin Y, Hu M, Weinreb V, Vachette P, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW Jr, J Mol Biol. 2003 Jan 3;325(1):39-63. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12473451 12473451]
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Tryptophan--tRNA ligase]]
[[Category: Bricogne G]]
[[Category: Bricogne, G.]]
[[Category: Carter Jr CW]]
[[Category: Hu, M.]]
[[Category: Hu M]]
[[Category: Huang, X.]]
[[Category: Huang X]]
[[Category: Ilyin, V.]]
[[Category: Ilyin V]]
[[Category: Jr., C.W.Carter.]]
[[Category: Retailleau P]]
[[Category: Retailleau, P.]]
[[Category: Roversi P]]
[[Category: Roversi, P.]]
[[Category: Vachette P]]
[[Category: Vachette, P.]]
[[Category: Vonrhein C]]
[[Category: Vonrhein, C.]]
[[Category: Weinreb V]]
[[Category: Weinreb, V.]]
[[Category: Yin Y]]
[[Category: Yin, Y.]]
[[Category: TRP]]
[[Category: amino acid binding site]]
[[Category: aminoacyl-trna synthetase]]
[[Category: rossmann fold]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:17:30 2007''

Latest revision as of 10:42, 14 February 2024

Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open ConformationCrystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation

Structural highlights

1mb2 is a 6 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYW_GEOSE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1mb2, resolution 2.70Å

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OCA
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