References for structures of protein-DNA complexes

BIOC/MCB 568 -- Fall 2010
John W. Little--University of Arizona

BIOC/MCB568 Home Page

 References

Review

Garvie, C.W. and Wolberger, C., Mol. Cell 8, 937–946 (2001). "Recognition of specific DNA sequences".

Specificity and energetics

von Hippel, P.H. and Berg, O.G., PNAS 83,1608-1612 (1986). "On the specificity of DNA-protein interactions".

Helix-turn-helix proteins

Mondragón, A. and Harrison, S.C. J. Mol. Biol. 219, 321-334 (1991). "The phage 434 Cro/oR1 complex at 2.5 Å resolution".

Beamer, L.J. and Pabo, C.O. J. Mol. Biol. 227, 177-196 (1992). "Refined 1.8 Å crystal structure of the lambda repressor-operator complex."

Schultz, S.C., Shields, G.C. and Steitz, T.A. Science 253, 1001-1007 (1991)."Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees." (link from U of A computers only)

Parkinson, G. et al. J. Mol.Biol. 260, 395-408 (1996). "Structure of the CAP- DNA complex at 2.5Å resolution: A complete picture of the protein-DNA interface."

Bell, C. E. and Lewis, M. J.Mol.Biol. 312, 921-926 (2001). "Crystallographic analysis of Lac repressor bound to natural operator O1."

Bell, C. E. and Lewis, M. Nat.Struct.Biol. 7, 209-214 (2000). "A closer view of the conformation of the Lac repressor bound to operator."

Passner, J. M., Ryoo, H. D., Shen, L., Mann, R. S., and Aggarwal, A. K. Nature 397, 714-719 (1999). "Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex ." Both proteins are homeodomain proteins (a type of HTH protein); this is a heterodimer of two proteins. Extradenticle confers more affinity and specificity on Ultrabithorax and other factors important in Drosophila development.

Piper, D. E., Batchelor, A. H., Chang, C. P., Cleary, M. L., and Wolberger, C. Cell 96, 587-597 (1999). "Structure of a HoxB1-Pbx1 heterodimer bound to DNA: Role of the hexapeptide and a fourth homeodomain helix in complex formation." This complex is of the human homolog of the Drosophila proteins in the previous paper.

Zinc finger proteins

Pavletich, N. and Pabo, C.O. Science 252, 809-817 (1991). "Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å". This protein is of the Cys2-His2 type.

Luisi, Xu, Otwinowski, Freedman, Yamamoto and Sigler, Nature 352, 497-505 (1991). "Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA". As with the engrailed peptide above, the protein is a small DNA-binding domain of a much larger protein. This peptide is of the Cys4 type.

Rastinejad, F., Wagner, T., Zhao, Q., and Khorasanizadeh, S. EMBO J. 19, 1045-1054 (2000). "Structure of the RXR-RAR DNA-binding complex on the retinoic acid response element DR1." Another hormone receptor, in this case a heterodimer.

Leucine zipper proteins

Ellenberger, T.E., Brandl, C.J., Struhl, K. and Harrison, S.C. Cell 71,1223-1237 (1992). "The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted helices: Crystal structure of the protein-DNA complex."

König, P. and Richmond, T.J. J. Mol. Biol. 233,139-154 (1993). "The X-ray structure of the GCN4-bZIP bound to ATF/CREB site DNA shows the complex depends on DNA flexibility."

Glover, J.N.M. and Harrison, S.C. Nature 373, 257-261 (1995). "Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA".

Keller, W., König, P., and Richmond, T. J. J. Mol. Biol. 254, 657-667 (1995). Crystal structure of a bZIP/DNA complex at 2.2 Å: Determinants of DNA specific recognition.

Helix-loop-helix proteins

Ferré-D'Amaré, A.R., Prendergast, G.C., Ziff, E.B. and Burley, S.K. Nature 363, 38-45 (1993). "Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain." This protein is one of several that have a helix-loop-helix followed by a leucine zipper.

Ellenberger, T., Fass, D., Arnaud, M. and Harrison, S.C. Genes Dev. 8, 970-980 (1994). "Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer." No leucine zipper in this protein or MyoD (next ref).

Ma, P.C.M., Rould, M.A., Weintraub, H. and Pabo, C.O. Cell 77, 451-459 (1994). "Crystal structure of MyoD bHLH domain-DNA complex: Perspectives on DNA recognition and implications for transcriptional activation."

Beta-sheet DNA-binding proteins:

Somers, W.S. and Phillips, S.E.V. Nature 359, 387-393 (1992). "Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by beta-strands."

Raumann, B.E., Rould, M.A., Pabo, C.O. and Sauer, R.T. Nature 367, 754-757 (1994). "DNA recognition by beta-sheets in the Arc repressor-operator crystal structure."

Biologically important proteins that don't fall into any of the common motifs:

Cho, Y., Gorina, S., Jeffrey, P.D. and Pavletich, N.P. Science 265, 346-355 (1994). "Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations." (link from U of A computers only).

Kim, J.L., Nikolov, D.B. and Burley, S.K. Nature 365, 520-527 (1993). "Co-crystal structure of TBP recognizing the minor groove of a TATA element."

Kim, Y., Geiger, J.H., Hahn, S. and Sigler, P.B. Nature 365, 512-520 (1993). "Crystal structure of a yeast TBP/TATA-box complex."

Ghosh, G. et al. Nature 373, 303-310 (1995). "Structure of NF-kappaB p50 homodimer bound to a kappaB site."

Müller, C.W. et al., Nature 373, 311- 317 (1995). "Structure of the NF-B p50 homodimer bound to DNA"

Rice, P. A. et al. Cell 87,1295-1306 (1996). "Crystal structure of an IHF-DNA complex: A protein-induced DNA u-turn."

Chen, F. E., Huang, D. B., Chen, Y. Q., and Ghosh, G. Nature 391, 410-413 (1998). "Crystal structure of p50/p65 heterodimer of transcription factor NF-kappaB bound to DNA."

Chen, X., Vinkemeier, U., Zhao, Y. X. et al. Cell 93, 827-839 (1998). "Crystal structure of a tyrosine phosphorylated STAT-1 dimer bound to DNA." STAT proteins form dimers only when phosphorylated on tyrosine by a signal transduction pathway. The structure reveals how phosphorylation has this consequence.