Crystal structure of the yeast MATα2/MCM1/DNA ternary complex

The structure of a complex containing the homeodomain repressor protein MATα2 and the MADS-box transcription factor MCM1 bound to DNA has been determined by X-ray crystallography at 2.25 Å resolution. It reveals the protein–protein interactions responsible for cooperative binding of MATα2 and MCM1 to DNA. The otherwise flexible amino-terminal extension of the MATα2 homeodomain forms a β-hairpin that grips the MCM1 surface through parallel β-strand hydrogen bonds and close-packed, predominantly hydrophobic, side chains. DNA bending induced by MCM1 brings the two proteins closer together, facilitating their interaction. An unusual feature of the complex is that an eight-amino-acid sequence adopts an α-helical conformation in one of two copies of the MATα2 monomer and a β-strand conformation in the other. This ‘chameleon’ sequence of MATα2 may be important for recognizing natural operator sites.

[1]  A. Johnson,et al.  The carboxy-terminal tail of the homeo domain protein alpha 2 is required for function with a second homeo domain protein. , 1993, Genes & development.

[2]  M. Weiss,et al.  Electrostatics and hydration at the homeodomain-DNA interface: chemical probes of an interfacial water cavity. , 1997, Journal of molecular biology.

[3]  D. Tronrud.  Conjugate-direction minimization: an improved method for the refinement of macromolecules. , 1992, Acta crystallographica. Section A, Foundations of crystallography.

[4]  M. Hall,et al.  Homeo domain of the yeast repressor alpha 2 is a sequence-specific DNA-binding domain but is not sufficient for repression. , 1987, Science.

[5]  R. Sauer,et al.  Flexibility of the yeast alpha 2 repressor enables it to occupy the ends of its operator, leaving the center free. , 1988, Genes & development.

[6]  Dana L. Smith,et al.  A molecular mechanism for combinatorial control in yeast: MCM1 protein sets the spacing and orientation of the homeodomains of an α2 dimer , 1992, Cell.

[7]  Song Tan,et al.  Structure of serum response factor core bound to DNA , 1995, Nature.

[8]  R. Elble,et al.  Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells. , 1988, Journal of molecular biology.

[9]  Alexander D. Johnson,et al.  Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1 , 1989, Molecular and cellular biology.

[10]  H. Zhong,et al.  The yeast alpha2 and Mcm1 proteins interact through a region similar to a motif found in homeodomain proteins of higher eukaryotes , 1996, Molecular and cellular biology.

[11]  P. S. Kim,et al.  Context-dependent secondary structure formation of a designed protein sequence , 1996, Nature.

[12]  M. Kuo,et al.  Multiple phosphorylated forms of the Saccharomyces cerevisiae Mcm1 protein include an isoform induced in response to high salt concentrations , 1997, Molecular and cellular biology.

[13]  Rolf Hilgenfeld,et al.  An α to β conformational switch in EF-Tu , 1996 .

[14]  R Lavery,et al.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. , 1988, Journal of biomolecular structure & dynamics.

[15]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[16]  D Kindelberger,et al.  Cell cycle-regulated transcription of the CLB2 gene is dependent on Mcm1 and a ternary complex factor , 1995, Molecular and cellular biology.

[17]  A. Nordheim,et al.  Mcm1 is required to coordinate G2-specific transcription in Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[18]  Conrad C. Huang,et al.  The MIDAS display system , 1988 .

[19]  F. Dahlquist,et al.  Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy. , 1991, Genes & development.

[20]  G F Sprague,et al.  MCM1 point mutants deficient in expression of alpha-specific genes: residues important for interaction with alpha 1 , 1994, Molecular and cellular biology.

[21]  M. F. Perutz,et al.  Mutations make enzyme polymerize , 1997, Nature.

[22]  A. Johnson,et al.  Molecular mechanisms of cell-type determination in budding yeast. , 1995, Current opinion in genetics & development.

[23]  M. Primig,et al.  The DNA binding and oligomerization domain of MCM1 is sufficient for its interaction with other regulatory proteins. , 1991, The EMBO journal.

[24]  Richard Treisman,et al.  SRF and MCM1 have related but distinct DNA binding specificities , 1992, Nucleic Acids Res..

[25]  H. Zhong,et al.  The Yeast Homeodomain Protein MATα2 Shows Extended DNA binding Specificity in Complex with Mcm1* , 1997, The Journal of Biological Chemistry.

[26]  S Thirup,et al.  Helix unwinding in the effector region of elongation factor EF-Tu-GDP. , 1996, Structure.

[27]  B. Tye,et al.  Functional domains of the yeast transcription/replication factor MCM1. , 1991, Genes & development.

[28]  C. Keleher,et al.  The yeast cell-type-specific repressor α2 acts cooperatively with a non-cell-type-specific protein , 1988, Cell.

[29]  H. Wright.  The structural puzzle of how serpin serine proteinase inhibitors work , 1996, BioEssays : news and reviews in molecular, cellular and developmental biology.

[30]  C. Desplan,et al.  Homeodomain Proteins: Cooperating to be different , 1995, Current Biology.

[31]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[32]  A. Vershon,et al.  A short, disordered protein region mediates interactions between the homeodomain of the yeast α2 protein and the MCM1 protein , 1993, Cell.

[33]  H. Zhong,et al.  DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein , 1997, Molecular and cellular biology.

[34]  K. Nasmyth,et al.  A new role for MCM1 in yeast: cell cycle regulation of SW15 transcription. , 1991, Genes & development.

[35]  Kurt Wüthrich,et al.  Homeodomain-DNA recognition , 1994, Cell.

[36]  K. Komachi,et al.  The WD repeats of Tup1 interact with the homeo domain protein alpha 2. , 1994, Genes & development.

[37]  C. Wolberger,et al.  Crystal Structure of the MATa1/MATα2 Homeodomain Heterodimer Bound to DNA , 1995, Science.

[38]  A. Sharrocks,et al.  The MADS-box family of transcription factors. , 1995, European journal of biochemistry.

[39]  A. Vershon.  Protein interactions of homeodomain proteins. , 1996, Current opinion in biotechnology.

[40]  Cynthia Wolberger,et al.  Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. , 1991, Cell.