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Induced fit and "lock and key" recognition of 5S RNA by zinc fingers of transcription factor IIIA.

Lee BM, Xu J, Clarkson BK, Martinez-Yamout MA, Dyson HJ, Case DA, Gottesfeld JM, Wright PE
J Mol Biol 357 275-91 (2006)
Cited: 50 times
EuropePMC logo PMID: 16405997

Abstract

Transcription factor IIIA (TFIIIA) is a Cys2His2 zinc finger protein that regulates expression of the 5 S ribosomal RNA gene by binding specifically to the internal control element. TFIIIA also functions in transport and storage of 5 S RNA by binding directly to the RNA transcript. To obtain insights into the mechanism by which TFIIIA recognizes 5 S RNA, we determined the solution structure of the middle three zinc fingers bound to the central core of 5 S RNA. Finger 4 utilizes "lock and key" recognition to bind in the widened major groove of the pre-structured RNA loop E motif. This interaction is mediated by direct hydrogen bonding interactions with bases. In contrast, recognition of loop A, a flexible junction of three helices, occurs by an induced fit mechanism that involves reorganization of the conserved CAUA motif and structuring of the finger 5-finger 6 interface to form a complementary RNA binding surface.

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  1. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Hum Genomics 6 10 (2012)

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  1. Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Zheng G, Lu XJ, Olson WK. Nucleic Acids Res 37 W240-6 (2009)
  2. Origins of coevolution between residues distant in protein 3D structures. Anishchenko I, Ovchinnikov S, Kamisetty H, Baker D. Proc Natl Acad Sci U S A 114 9122-9127 (2017)
  3. A nonredundant structure dataset for benchmarking protein-RNA computational docking. Huang SY, Zou X. J Comput Chem 34 311-318 (2013)
  4. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. Jain S, Schlick T. J Mol Biol 429 3587-3605 (2017)
  5. A pipeline for computational design of novel RNA-like topologies. Jain S, Laederach A, Ramos SBV, Schlick T. Nucleic Acids Res 46 7040-7051 (2018)
  6. From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces. Shazman S, Elber G, Mandel-Gutfreund Y. Nucleic Acids Res 39 7390-7399 (2011)
  7. Patterns of coevolving amino acids unveil structural and dynamical domains. Granata D, Ponzoni L, Micheletti C, Carnevale V. Proc Natl Acad Sci U S A 114 E10612-E10621 (2017)
  8. Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. Bayrak CS, Kim N, Schlick T. Nucleic Acids Res 45 5414-5422 (2017)
  9. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. Pröpper K, Meindl K, Sammito M, Dittrich B, Sheldrick GM, Pohl E, Usón I. Acta Crystallogr D Biol Crystallogr 70 1743-1757 (2014)
  10. RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling. Li J, Chen SJ. Nucleic Acids Res 51 3341-3356 (2023)
  11. Dual-wield NTPases: A novel protein family mined from AlphaFold DB. Sakuma K, Koike R, Ota M. Protein Sci 33 e4934 (2024)


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  1. RNA-binding proteins: modular design for efficient function. Lunde BM, Moore C, Varani G. Nat Rev Mol Cell Biol 8 479-490 (2007)
  2. What macromolecular crowding can do to a protein. Kuznetsova IM, Turoverov KK, Uversky VN. Int J Mol Sci 15 23090-23140 (2014)
  3. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Brayer KJ, Segal DJ. Cell Biochem Biophys 50 111-131 (2008)
  4. Intrinsically disordered proteins and their environment: effects of strong denaturants, temperature, pH, counter ions, membranes, binding partners, osmolytes, and macromolecular crowding. Uversky VN. Protein J 28 305-325 (2009)
  5. Eukaryotic 5S rRNA biogenesis. Ciganda M, Williams N. Wiley Interdiscip Rev RNA 2 523-533 (2011)
  6. Roles of intrinsic disorder in protein-nucleic acid interactions. Dyson HJ. Mol Biosyst 8 97-104 (2012)
  7. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FH. Prog Nucl Magn Reson Spectrosc 58 1-61 (2011)
  8. Intrinsically disordered proteins in crowded milieu: when chaos prevails within the cellular gumbo. Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Cell Mol Life Sci 75 3907-3929 (2018)
  9. Proteins without unique 3D structures: biotechnological applications of intrinsically unstable/disordered proteins. Uversky VN. Biotechnol J 10 356-366 (2015)
  10. A structural perspective on RNA polymerase I and RNA polymerase III transcription machineries. Vannini A. Biochim Biophys Acta 1829 258-264 (2013)
  11. Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes. Appels R, Wang P, Islam S. Front Plant Sci 12 686586 (2021)

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  1. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Parisien M, Major F. Nature 452 51-55 (2008)
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  3. Structure of the 5' nontranslated region of the coxsackievirus b3 genome: Chemical modification and comparative sequence analysis. Bailey JM, Tapprich WE. J Virol 81 650-668 (2007)
  4. Genome-Wide Analysis of C2H2 Zinc-Finger Family Transcription Factors and Their Responses to Abiotic Stresses in Poplar (Populus trichocarpa). Liu Q, Wang Z, Xu X, Zhang H, Li C. PLoS One 10 e0134753 (2015)
  5. The protein-binding potential of C2H2 zinc finger domains. Brayer KJ, Kulshreshtha S, Segal DJ. Cell Biochem Biophys 51 9-19 (2008)
  6. Chaperoning 5S RNA assembly. Madru C, Lebaron S, Blaud M, Delbos L, Pipoli J, Pasmant E, Réty S, Leulliot N. Genes Dev 29 1432-1446 (2015)
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  8. Pre-folding IkappaBalpha alters control of NF-kappaB signaling. Truhlar SM, Mathes E, Cervantes CF, Ghosh G, Komives EA. J Mol Biol 380 67-82 (2008)
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  11. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. Biochemistry 45 11776-11789 (2006)
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  14. Dicistronic tRNA-5S rRNA genes in Yarrowia lipolytica: an alternative TFIIIA-independent way for expression of 5S rRNA genes. Acker J, Ozanne C, Kachouri-Lafond R, Gaillardin C, Neuvéglise C, Marck C. Nucleic Acids Res 36 5832-5844 (2008)
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  22. Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, He Y. Mol Cell 83 2641-2652.e7 (2023)
  23. The structural properties of DNA regulate gene expression. Soltani S, Askari H, Ejlali N, Aghdam R. Mol Biosyst 10 273-280 (2014)
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  27. Structural analysis of zinc-finger (TTK) + [Cu(BPA)]2+ /[Cu(IDB)]2+ + DNA complexes: an investigation by molecular dynamics simulation. Wang Y, Zhu Y, Wang Y, Chen G. J Mol Recognit 24 981-994 (2011)


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