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Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2.

Sivaraja M, Botfield MC, Mueller M, Jancso A, Weiss MA
Biochemistry 33 9845-55 (1994)
Cited: 27 times
EuropePMC logo PMID: 7914745

Abstract

The POU DNA-binding motif defines a conserved family of eukaryotic transcription factors involved in regulation of gene expression. This bipartite motif consists of an N-terminal POU-specific domain (POUs), a flexible linker, and a C-terminal POU-specific homeodomain (POUHD). Here we describe the solution structure of a POU-specific homeodomain. An NMR model is obtained from Oct-2, a human B-cell specific transcription factor which participates in the regulation of immunoglobulin genes. A fragment of Oct-2 containing POUHD and an adjoining linker was expressed in Escherichia coli and characterized by three-dimensional nuclear magnetic resonance (3D-NMR) spectroscopy. Complete 1H and 15N resonance assignment of the POUHD moiety is presented. The POUHD solution structure, as calculated by distance geometry and simulated annealing (DG/SA), is similar to that of canonical homeodomains. A salient difference between solution and crystal structures is observed in the C-terminal segment of alpha-helix 3 (the HTH recognition helix), which is not well ordered in solution. Because this segment presumably folds upon specific DNA binding, its flexibility in solution may reduce the intrinsic DNA affinity of POUHD in the absence of POUs.

Articles - 1hdp mentioned but not cited (5)

  1. Packing helices in proteins by global optimization of a potential energy function. Nanias M, Chinchio M, Pillardy J, Ripoll DR, Scheraga HA. Proc. Natl. Acad. Sci. U.S.A. 100 1706-1710 (2003)
  2. CK2 phosphorylation of the PRH/Hex homeodomain functions as a reversible switch for DNA binding. Soufi A, Noy P, Buckle M, Sawasdichai A, Gaston K, Jayaraman PS. Nucleic Acids Res. 37 3288-3300 (2009)
  3. The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins. Chakraborty S, Rendón-Ramírez A, Ásgeirsson B, Dutta M, Ghosh AS, Oda M, Venkatramani R, Rao BJ, Dandekar AM, Goñi FM. F1000Res 2 286 (2013)
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  5. Exploring protein structural dissimilarity to facilitate structure classification. Jain P, Hirst JD. BMC Struct. Biol. 9 60 (2009)


Reviews citing this publication (3)

  1. The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation. Herr W. Cold Spring Harb. Symp. Quant. Biol. 63 599-607 (1998)
  2. Analysis and design of three-stranded coiled coils and three-helix bundles. Schneider JP, Lombardi A, DeGrado WF. Fold Des 3 R29-40 (1998)
  3. Towards a mutant analysis of the tertiary structures of functional DNA-binding motifs. Barker A, Müller-Hill B. FEBS Lett. 432 1-3 (1998)

Articles citing this publication (19)

  1. Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandoski MM, Record MT. J. Mol. Biol. 267 1186-1206 (1997)
  2. Refined crystal structures of native human angiogenin and two active site variants: implications for the unique functional properties of an enzyme involved in neovascularisation during tumour growth. Leonidas DD, Shapiro R, Allen SC, Subbarao GV, Veluraja K, Acharya KR. J. Mol. Biol. 285 1209-1233 (1999)
  3. Coactivator OBF-1 makes selective contacts with both the POU-specific domain and the POU homeodomain and acts as a molecular clamp on DNA. Sauter P, Matthias P. Mol. Cell. Biol. 18 7397-7409 (1998)
  4. Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain. Cleary MA, Herr W. Mol. Cell. Biol. 15 2090-2100 (1995)
  5. Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1. Li H, Tejero R, Monleon D, Bassolino-Klimas D, Abate-Shen C, Bruccoleri RE, Montelione GT. Protein Sci. 6 956-970 (1997)
  6. The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site. Baird-Titus JM, Clark-Baldwin K, Dave V, Caperelli CA, Ma J, Rance M. J. Mol. Biol. 356 1137-1151 (2006)
  7. Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation. Ahmad I, Hoessli DC, Walker-Nasir E, Rafik SM, Shakoori AR, Nasir-ud-Din. Nucleic Acids Res. 34 175-184 (2006)
  8. Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics. Esposito G, Fogolari F, Damante G, Formisano S, Tell G, Leonardi A, Di Lauro R, Viglino P. Eur. J. Biochem. 241 101-113 (1996)
  9. Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC. Suzuki M, Brenner SE. FEBS Lett. 372 215-221 (1995)
  10. Solution structure of the Oct-1 POU homeodomain determined by NMR and restrained molecular dynamics. Cox M, van Tilborg PJ, de Laat W, Boelens R, van Leeuwen HC, van der Vliet PC, Kaptein R. J. Biomol. NMR 6 23-32 (1995)
  11. All known in vivo functions of the Oct-2 transcription factor require the C-terminal protein domain. Corcoran LM, Koentgen F, Dietrich W, Veale M, Humbert PO. J Immunol 172 2962-2969 (2004)
  12. Mutation of the Oct-1 POU-specific recognition helix leads to altered DNA binding and influences enhancement of adenovirus DNA replication. van Leeuwen HC, Strating MJ, Cox M, Kaptein R, van der Vliet PC. Nucleic Acids Res. 23 3189-3197 (1995)
  13. Analysis of the conformation and stability of rat TTF-1 homeodomain by circular dichroism. Damante G, Tell G, Leonardi A, Fogolari F, Bortolotti N, Di Lauro R, Formisano S. FEBS Lett. 354 293-296 (1994)
  14. Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction. Keasar C, Elber R, Skolnick J. Fold Des 2 247-259 (1997)
  15. The solution structure of the homeodomain of the rat insulin-gene enhancer protein isl-1. Comparison with other homeodomains. Ippel H, Larsson G, Behravan G, Zdunek J, Lundqvist M, Schleucher J, Lycksell PO, Wijmenga S. J. Mol. Biol. 288 689-703 (1999)
  16. Optimal Oct-2 affinity for an extended DNA site and the effect of GST fusion on site preference. Rhee JM, Trieu M, Turner EE. Arch. Biochem. Biophys. 385 397-405 (2001)
  17. Structure of the Oct-3 POU-homeodomain in solution, as determined by triple resonance heteronuclear multidimensional NMR spectroscopy. Morita EH, Shirakawa M, Hayashi F, Imagawa M, Kyogoku Y. Protein Sci. 4 729-739 (1995)
  18. Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations. Iurcu-Mustata G, Van Belle D, Wintjens R, Prévost M, Rooman M. Biopolymers 59 145-159 (2001)
  19. Hydrogen-deuterium exchange studies of the rat thyroid transcription factor 1 homeodomain. Esposito G, Fogolari F, Damante G, Formisano S, Tell G, Leonardi A, Di Lauro R, Viglino P. J. Biomol. NMR 9 397-407 (1997)


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