Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy

1991 ◽  
Vol 113 (12) ◽  
pp. 4371-4380 ◽  
Author(s):  
Arthur G. Palmer ◽  
Mark Rance ◽  
Peter E. Wright
Keyword(s):  
Nmr Spectroscopy ◽  
Dna Binding ◽  
Zinc Finger ◽  
Heteronuclear Nmr ◽  
Binding Domain ◽  
Natural Abundance ◽  
Dna Binding Domain ◽  
Heteronuclear Nmr Spectroscopy ◽  
Intramolecular Motions

scholarly journals The C6 zinc finger and adjacent amino acids determine DNA-binding specificity and affinity in the yeast activator proteins LAC9 and PPR1.

1990 ◽  
Vol 10 (10) ◽  
pp. 5128-5137 ◽  
Author(s):  
M M Witte ◽  
R C Dickson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Binding Specificity ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Transcription Activator ◽  
Activator Proteins ◽  
Dna Binding Specificity

LAC9 is a DNA-binding protein that regulates transcription of the lactose-galactose regulon in Kluyveromyces lactis. The DNA-binding domain is composed of a zinc finger and nearby amino acids (M. M. Witte and R. C. Dickson, Mol. Cell. Biol. 8:3726-3733, 1988). The single zinc finger appears to be structurally related to the zinc finger of many other fungal transcription activator proteins that contain positively charged residues and six conserved cysteines with the general form Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-9-Cys-Xaa2-Cys-Xaa 6-Cys, where Xaan indicates a stretch of the indicated number of any amino acids (R. M. Evans and S. M. Hollenberg, Cell 52:1-3, 1988). The function(s) of the zinc finger and other amino acids in DNA-binding remains unclear. To determine which portion of the LAC9 DNA-binding domain mediates sequence recognition, we replaced the C6 zinc finger, amino acids adjacent to the carboxyl side of the zinc finger, or both with the analogous region from the Saccharomyces cerevisiae PPR1 or LEU3 protein. A chimeric LAC9 protein, LAC9(PPR1 34-61), carrying only the PPR1 zinc finger, retained the DNA-binding specificity of LAC9. However, LAC9(PPR1 34-75), carrying the PPR1 zinc finger and 14 amino acids on the carboxyl side of the zinc finger, gained the DNA-binding specificity of PPR1, indicating that these 14 amino acids are necessary for specific DNA binding. Our data show that C6 fingers can substitute for each other and allow DNA binding, but binding affinity is reduced. Thus, in a qualitative sense C6 fingers perform a similar function(s). However, the high-affinity binding required by natural C6 finger proteins demands a unique C6 finger with a specific amino acid sequence. This requirement may reflect conformational constraints, including interactions between the C6 finger and the carboxyl-adjacent amino acids; alternatively or in addition, it may indicate that unique, nonconserved amino acid residues in zinc fingers make sequence-specifying or stabilizing contacts with DNA.

A position-dependent transcription-activating domain in TFIIIA

1993 ◽  
Vol 13 (12) ◽  
pp. 7496-7506
Author(s):  
X Mao ◽  
M K Darby
Keyword(s):  
Amino Acids ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Zinc Finger ◽  
Transcriptional Activation ◽  
Transcriptional Activity ◽  
Rna Polymerase Iii ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
5S Rna

Transcription of the Xenopus 5S RNA gene by RNA polymerase III requires the gene-specific factor TFIIIA. To identify domains within TFIIIA that are essential for transcriptional activation, we have expressed C-terminal deletion, substitution, and insertion mutants of TFIIIA in bacteria as fusions with maltose-binding protein (MBP). The MBP-TFIIIA fusion protein specifically binds to the 5S RNA gene internal control region and complements transcription in a TFIIIA-depleted oocyte nuclear extract. Random, cassette-mediated mutagenesis of the carboxyl region of TFIIIA, which is not required for promoter binding, has defined a 14-amino-acid region that is critical for transcriptional activation. In contrast to activators of RNA polymerase II, the activity of the TFIIIA activation domain is strikingly sensitive to its position relative to the DNA-binding domain. When the eight amino acids that separate the transcription-activating domain from the last zinc finger are deleted, transcriptional activity is lost. Surprisingly, diverse amino acids can replace these eight amino acids with restoration of full transcriptional activity, suggesting that the length and not the sequence of this region is important. Insertion of amino acids between the zinc finger region and the transcription-activating domain causes a reduction in transcription proportional to the number of amino acids introduced. We propose that to function, the transcription-activating domain of TFIIIA must be correctly positioned at a minimum distance from the DNA-binding domain.

scholarly journals Secondary structure and folding topology of the DNA binding domain of interferon regulatory factor 2, as revealed by NMR spectroscopy

FEBS Letters ◽  
1995 ◽  
Vol 359 (2-3) ◽  
pp. 184-188 ◽  
Author(s):  
Koichi Uegaki ◽  
Masahiro Shirakawa ◽  
Hisashi Harada ◽  
Tadatsugu Taniguchi ◽  
Yoshimasa Kyogoku
Keyword(s):  
Nmr Spectroscopy ◽  
Secondary Structure ◽  
Dna Binding ◽  
Interferon Regulatory Factor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Regulatory Factor

The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain

2004 ◽  
Vol 37 (5) ◽  
pp. 741-749 ◽  
Author(s):  
Yoshimi Umemura ◽  
Tomoko Ishiduka ◽  
Rie Yamamoto ◽  
Muneharu Esaka
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Higher Plants ◽  
Binding Domain ◽  
Dna Binding Domain

scholarly journals A New Coactivator Function for Zac1's C2H2 Zinc Finger DNA-Binding Domain in Selectively Controlling PCAF Activity

2008 ◽  
Vol 28 (19) ◽  
pp. 6078-6093 ◽  
Author(s):  
Anke Hoffmann ◽  
Dietmar Spengler
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Zinc Finger ◽  
Transcriptional Control ◽  
Zinc Finger Protein ◽  
Embryonic Stem ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Histone H4 ◽  
Histone H4 Acetylation

ABSTRACT The generally accepted paradigm of transcription by regulated recruitment defines sequence-specific transcription factors and coactivators as separate categories that are distinguished by their abilities to bind DNA autonomously. The C2H2 zinc finger protein Zac1, with an established role in canonical DNA binding, also acts as a coactivator. Commensurate with this function, p73, which is related to p53, is here shown to recruit Zac1, together with the coactivators p300 and PCAF, to the p21Cip1 promoter during the differentiation of embryonic stem cells into neurons. In the absence of autonomous DNA binding, Zac1's zinc fingers stabilize the association of PCAF with p300, suggesting its scaffolding function. Furthermore, Zac1 regulates the affinities of PCAF substrates as well as the catalytic activities of PCAF to induce a selective switch in favor of histone H4 acetylation and thereby the efficient transcription of p21Cip1. These results are consistent with an authentic coactivator function of Zac1's C2H2 zinc finger DNA-binding domain and suggest coactivation by sequence-specific transcription factors as a new facet of transcriptional control.

scholarly journals Obesity-induced protein carbonylation in murine adipose tissue regulates the DNA-binding domain of nuclear zinc finger proteins

2018 ◽  
Vol 293 (35) ◽  
pp. 13464-13476 ◽  
Author(s):  
Amy K. Hauck ◽  
Tong Zhou ◽  
Wendy Hahn ◽  
Raphael Petegrosso ◽  
Rui Kuang ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Dna Binding ◽  
Zinc Finger ◽  
Zinc Finger Proteins ◽  
Protein Carbonylation ◽  
Binding Domain ◽  
Dna Binding Domain

scholarly journals Unique Structure of the DNA Binding Domain of Interferon Regulatory Factor 2 Determined by NMR Spectroscopy.

1994 ◽  
Vol 70 (10) ◽  
pp. 200-204
Author(s):  
Koichi UEGAKI ◽  
Masahiro SHIRAKAWA ◽  
Hisashi HARADA ◽  
Tadatsugu TANIGUCHI ◽  
Yoshimasa KYOGOKU
Keyword(s):  
Nmr Spectroscopy ◽  
Dna Binding ◽  
Interferon Regulatory Factor ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Regulatory Factor ◽  
Unique Structure
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