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| | ==Solution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae== | | ==Solution structure of the intermembrane space domain of the mitochondrial import protein Tim21 from S. cerevisiae== |
| - | <StructureSection load='6k8q' size='340' side='right'caption='[[6k8q]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='6k8q' size='340' side='right'caption='[[6k8q]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6k8q]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K8Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6k8q]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K8Q FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TIM21, YGR033C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr> | + | </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=6k8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8q OCA], [https://pdbe.org/6k8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k8q RCSB], [https://www.ebi.ac.uk/pdbsum/6k8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8q ProSAT]</span></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=6k8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k8q OCA], [http://pdbe.org/6k8q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k8q RCSB], [http://www.ebi.ac.uk/pdbsum/6k8q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k8q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TIM21_YEAST TIM21_YEAST]] Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to keep the TOM and the TIM23 complexes in close contact. At some point, it is released from the TOM23 complex to allow protein translocation into the mitochondrial matrix. In the complex, it acts as an antagonist of TIM50 by reducing preprotein accumulation at the TOM23 complex and promotes dissociation of the PAM complex from the TIM23 complex.<ref>PMID:15797382</ref> <ref>PMID:15878866</ref> | + | [https://www.uniprot.org/uniprot/TIM21_YEAST TIM21_YEAST] Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to keep the TOM and the TIM23 complexes in close contact. At some point, it is released from the TOM23 complex to allow protein translocation into the mitochondrial matrix. In the complex, it acts as an antagonist of TIM50 by reducing preprotein accumulation at the TOM23 complex and promotes dissociation of the PAM complex from the TIM23 complex.<ref>PMID:15797382</ref> <ref>PMID:15878866</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bala, S]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Kobayashi, N]] | + | [[Category: Bala S]] |
| - | [[Category: Kohda, D]] | + | [[Category: Kobayashi N]] |
| - | [[Category: Kojima, C]] | + | [[Category: Kohda D]] |
| - | [[Category: Miyashita, O]] | + | [[Category: Kojima C]] |
| - | [[Category: Shimada, A]] | + | [[Category: Miyashita O]] |
| - | [[Category: Shinya, S]] | + | [[Category: Shimada A]] |
| - | [[Category: Srivastava, A]] | + | [[Category: Shinya S]] |
| - | [[Category: Tama, F]] | + | [[Category: Srivastava A]] |
| - | [[Category: Membrane]]
| + | [[Category: Tama F]] |
| - | [[Category: Mitochondria]]
| + | |
| - | [[Category: Protein transport]]
| + | |
| - | [[Category: Translocation]]
| + | |
| Structural highlights
Function
TIM21_YEAST Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to keep the TOM and the TIM23 complexes in close contact. At some point, it is released from the TOM23 complex to allow protein translocation into the mitochondrial matrix. In the complex, it acts as an antagonist of TIM50 by reducing preprotein accumulation at the TOM23 complex and promotes dissociation of the PAM complex from the TIM23 complex.[1] [2]
Publication Abstract from PubMed
BACKGROUND: In protein crystals, flexible loops are frequently deformed by crystal contacts, whereas in solution, the large motions result in the poor convergence of such flexible loops in NMR structure determinations. We need an experimental technique to characterize the structural and dynamic properties of intrinsically flexible loops of protein molecules. METHODS: We designed an intended crystal contact-free space (CCFS) in protein crystals, and arranged the flexible loop of interest in the CCFS. The yeast Tim 21 protein was chosen as the model protein, because one of the loops (loop 2) is distorted by crystal contacts in the conventional crystal. RESULTS: Yeast Tim21 was fused to the MBP protein by a rigid alpha-helical linker. The space created between the two proteins was used as the CCFS. The linker length provides adjustable freedom to arrange loop 2 in the CCFS. We re-determined the NMR structure of yeast Tim21, and conducted MD simulations for comparison. Multidimensional scaling was used to visualize the conformational similarity of loop 2. We found that the crystal contact-free conformation of loop 2 is located close to the center of the ensembles of the loop 2 conformations in the NMR and MD structures. CONCLUSIONS: Loop 2 of yeast Tim21 in the CCFS adopts a representative, dominant conformation in solution. GENERAL SIGNIFICANCE: No single powerful technique is available for the characterization of flexible structures in protein molecules. NMR analyses and MD simulations provide useful, but incomplete information. CCFS crystallography offers a third route to this goal.
Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study.,Bala S, Shinya S, Srivastava A, Ishikawa M, Shimada A, Kobayashi N, Kojima C, Tama F, Miyashita O, Kohda D Biochim Biophys Acta Gen Subj. 2020 Feb;1864(2):129418. doi:, 10.1016/j.bbagen.2019.129418. Epub 2019 Aug 23. PMID:31449839[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chacinska A, Lind M, Frazier AE, Dudek J, Meisinger C, Geissler A, Sickmann A, Meyer HE, Truscott KN, Guiard B, Pfanner N, Rehling P. Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17. Cell. 2005 Mar 25;120(6):817-29. PMID:15797382 doi:http://dx.doi.org/10.1016/j.cell.2005.01.011
- ↑ Mokranjac D, Popov-Celeketic D, Hell K, Neupert W. Role of Tim21 in mitochondrial translocation contact sites. J Biol Chem. 2005 Jun 24;280(25):23437-40. Epub 2005 May 4. PMID:15878866 doi:http://dx.doi.org/C500135200
- ↑ Bala S, Shinya S, Srivastava A, Ishikawa M, Shimada A, Kobayashi N, Kojima C, Tama F, Miyashita O, Kohda D. Crystal contact-free conformation of an intrinsically flexible loop in protein crystal: Tim21 as the case study. Biochim Biophys Acta Gen Subj. 2020 Feb;1864(2):129418. doi:, 10.1016/j.bbagen.2019.129418. Epub 2019 Aug 23. PMID:31449839 doi:http://dx.doi.org/10.1016/j.bbagen.2019.129418
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