Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

The x-ray structure of a C-terminal fragment of the RAP74 subunit of human transcription factor (TF) IIF has been determined at 1.02-Å resolution. The α/β structure is strikingly similar to the globular domain of linker histone H5 and the DNA-binding domain of hepatocyte nuclear factor 3γ (HNF-3γ), making it a winged-helix protein. The surface electrostatic properties of this compact domain differ significantly from those of bona fide winged-helix transcription factors (HNF-3γ and RFX1) and from the winged-helix domains found within the RAP30 subunit of TFIIF and the β subunit of TFIIE. RAP74 has been shown to interact with the TFIIF-associated C-terminal domain phosphatase FCP1, and a putative phosphatase binding site has been identified within the RAP74 winged-helix domain.

[1]  P. Cohen The structure and regulation of protein phosphatases. , 1989, Annual review of biochemistry.

[2]  R. Conaway,et al.  Transcription initiated by RNA polymerase II and purified transcription factors from liver. Transcription factors alpha, beta gamma, and delta promote formation of intermediates in assembly of the functional preinitiation complex. , 1990, The Journal of biological chemistry.

[3]  D. Hardie,et al.  Evidence that AMP triggers phosphorylation as well as direct allosteric activation of rat liver AMP-activated protein kinase. A sensitive mechanism to protect the cell against ATP depletion. , 1991, European journal of biochemistry.

[4]  R. Conaway,et al.  Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors alpha and beta gamma promote entry of polymerase into the preinitiation complex. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Mike Carson,et al.  RIBBONS 2.0 , 1991 .

[6]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

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

[8]  P. Sharp,et al.  RNA polymerase II-associated proteins are required for a DNA conformation change in the transcription initiation complex. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. Greenblatt,et al.  The general transcription factor RAP30 binds to RNA polymerase II and prevents it from binding nonspecifically to DNA , 1992, Molecular and cellular biology.

[10]  R. Sauer,et al.  Transcription factors: structural families and principles of DNA recognition. , 1992, Annual review of biochemistry.

[11]  D. Reinberg,et al.  Factors involved in specific transcription by mammalian RNA polymerase II. Identification and characterization of factor IIH. , 1992, The Journal of biological chemistry.

[12]  R. Conaway,et al.  General initiation factors for RNA polymerase II. , 1993, Annual review of biochemistry.

[13]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[14]  S. Burley,et al.  Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5 , 1993, Nature.

[15]  P. Sharp,et al.  DNA topology and a minimal set of basal factors for transcription by RNA polymerase II , 1993, Cell.

[16]  R. Conaway,et al.  Transcription factor SIII: a novel component of the RNA polymerase II elongation complex. , 1993, Cellular & molecular biology research.

[17]  V. Ramakrishnan,et al.  Crystal structure of globular domain of histone H5 and its implications for nucleosome binding , 1993, Nature.

[18]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[19]  M. Dahmus,et al.  Purification and characterization of a phosphatase from HeLa cells which dephosphorylates the C-terminal domain of RNA polymerase II. , 1994, The Journal of biological chemistry.

[20]  Joyce Li,et al.  Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. , 1994, The Journal of biological chemistry.

[21]  J. Greenblatt,et al.  Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. , 1994, The Journal of biological chemistry.

[22]  Z. Burton,et al.  The Activity of COOH-terminal Domain Phosphatase Is Regulated by a Docking Site on RNA Polymerase II and by the General Transcription Factors IIF and IIB (*) , 1995, The Journal of Biological Chemistry.

[23]  Steven L. Cohen,et al.  Probing the solution structure of the DNA‐binding protein Max by a combination of proteolysis and mass spectrometry , 1995, Protein science : a publication of the Protein Society.

[24]  F. Robert,et al.  Localization of Subunits of Transcription Factors IIE and IIF Immediately Upstream of the Transcriptional Initiation Site of the Adenovirus Major Late Promoter (*) , 1996, The Journal of Biological Chemistry.

[25]  C Sander,et al.  Mapping the Protein Universe , 1996, Science.

[26]  S. Fang,et al.  RNA Polymerase II-associated Protein (RAP) 74 Binds Transcription Factor (TF) IIB and Blocks TFIIB-RAP30 Binding (*) , 1996, The Journal of Biological Chemistry.

[27]  D. Barford,et al.  Crystal structure of the protein serine/threonine phosphatase 2C at 2.0 A resolution. , 1996, The EMBO journal.

[28]  D. Reinberg,et al.  Purification of human RNA polymerase II and general transcription factors. , 1996, Methods in enzymology.

[29]  C. Kane,et al.  Purification and Characterization of an RNA Polymerase II Phosphatase from Yeast* , 1996, The Journal of Biological Chemistry.

[30]  R. Roeder,et al.  The role of general initiation factors in transcription by RNA polymerase II. , 1996, Trends in biochemical sciences.

[31]  G. Sheldrick,et al.  SHELXL: high-resolution refinement. , 1997, Methods in enzymology.

[32]  J. Greenblatt,et al.  An essential component of a C-terminal domain phosphatase that interacts with transcription factor IIF in Saccharomyces cerevisiae. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[34]  D. Tillman,et al.  Monoclonal anti-DNA antibodies: structure, specificity, and biology. , 1997, Methods.

[35]  Shake-and-bake: an algorithm for automatic solution ab initio of crystal structures. , 1997, Methods in enzymology.

[36]  F. Robert,et al.  Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF. , 1998, Molecular cell.

[37]  K. Taylor,et al.  Crystal structure of the cyanobacterial metallothionein repressor SmtB: a model for metalloregulatory proteins. , 1998, Journal of molecular biology.

[38]  S. Oshiro,et al.  Structure of the human transcription factor TFIIF revealed by limited proteolysis with trypsin , 1998, FEBS letters.

[39]  M. H. Werner,et al.  Structural homology between the Rap30 DNA-binding domain and linker histone H5: implications for preinitiation complex assembly. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Z. Burton,et al.  Functions of the N- and C-Terminal Domains of Human RAP74 in Transcriptional Initiation, Elongation, and Recycling of RNA Polymerase II , 1998, Molecular and Cellular Biology.

[41]  F. Tirode,et al.  Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7. , 1999, Molecular cell.

[42]  D. Reinberg,et al.  A protein phosphatase functions to recycle RNA polymerase II. , 1999, Genes & development.

[43]  D. Reinberg,et al.  Mechanism of ATP-dependent promoter melting by transcription factor IIH. , 2000, Science.

[44]  T. Richmond,et al.  Novel dimerization fold of RAP30/RAP74 in human TFIIF at 1.7 A resolution. , 2000, Journal of molecular biology.

[45]  Stephen K. Burley,et al.  Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding , 2000, Nature.

[46]  J. Greenblatt,et al.  A Motif Shared by TFIIF and TFIIB Mediates Their Interaction with the RNA Polymerase II Carboxy-Terminal Domain Phosphatase Fcp1p in Saccharomyces cerevisiae , 2000, Molecular and Cellular Biology.

[47]  F. Hanaoka,et al.  Structure of the central core domain of TFIIEβ with a novel double‐stranded DNA‐binding surface , 2000, The EMBO journal.