|
|
| (3 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| | + | |
| | ==Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus== | | ==Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus== |
| - | <StructureSection load='4qvi' size='340' side='right' caption='[[4qvi]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='4qvi' size='340' side='right'caption='[[4qvi]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4qvi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QVI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4qvi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QVI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3u4m|3u4m]], [[3umy|3umy]], [[3u42|3u42]], [[3u56|3u56]], [[4qgb|4qgb]], [[4qg3|4qg3]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PRD_900003:sucrose'>PRD_900003</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qvi RCSB], [http://www.ebi.ac.uk/pdbsum/4qvi PDBsum]</span></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=4qvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qvi OCA], [https://pdbe.org/4qvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qvi RCSB], [https://www.ebi.ac.uk/pdbsum/4qvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qvi ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RL1_THETH RL1_THETH]] The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Binds directly to 23S rRNA.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318] | + | [https://www.uniprot.org/uniprot/RL1_THETH RL1_THETH] The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Binds directly to 23S rRNA.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 17: |
Line 18: |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4qvi" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosomal protein L1|Ribosomal protein L1]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Gabdulkhakov, A G]] | + | [[Category: Large Structures]] |
| - | [[Category: NIkonov, S V]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Nevskaya, N A]] | + | [[Category: Gabdulkhakov AG]] |
| - | [[Category: L1 protuberance]] | + | [[Category: NIkonov SV]] |
| - | [[Category: Ribosomal protein]] | + | [[Category: Nevskaya NA]] |
| - | [[Category: Ribosomal protein-rna complex]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Rrna]]
| + | |
| Structural highlights
4qvi is a 2 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.9Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
RL1_THETH The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Binds directly to 23S rRNA.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318]
Publication Abstract from PubMed
Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 from Thermus thermophilus (TthL1) in complex with a specific 80 nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein-RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA-protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity.
Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions.,Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):376-86. doi:, 10.1107/S1399004714026248. Epub 2015 Jan 23. PMID:25664749[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Tishchenko S, Kostareva O, Gabdulkhakov A, Mikhaylina A, Nikonova E, Nevskaya N, Sarskikh A, Piendl W, Garber M, Nikonov S. Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions. Acta Crystallogr D Biol Crystallogr. 2015 Feb;71(Pt 2):376-86. doi:, 10.1107/S1399004714026248. Epub 2015 Jan 23. PMID:25664749 doi:http://dx.doi.org/10.1107/S1399004714026248
|
