The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins

Science ◽  
1988 ◽  
Vol 240 (4860) ◽  
pp. 1759-1764 ◽  
Author(s):  
WH Landschulz ◽  
PF Johnson ◽  
SL McKnight
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Binding Proteins ◽  
Leucine Zipper ◽  
Regulatory Protein ◽  
Alpha Helix ◽  
Dna Binding Proteins ◽  
Amino Acid Sequences ◽  
Helical Conformation ◽  
Hypothetical Structure

A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.

scholarly journals Complete Amino-Acid Sequences of DNA-Binding Proteins HU-1 and HU-2 from Escherichia coli

1980 ◽  
Vol 103 (3) ◽  
pp. 456-461
Author(s):  
B. Laine ◽  
D. Kmiecik ◽  
P. Sautiere ◽  
G. Biserte ◽  
M. Cohen-Solal
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Amino Acid Sequences

Complete Amino-Acid Sequences of DNA-Binding Proteins HU-1 and HU-2 from Escherichia coli

1980 ◽  
Vol 103 (3) ◽  
pp. 447-461 ◽  
Author(s):  
Bernard LAINE ◽  
Daniel KMIECIK ◽  
Pierre SAUTIERE ◽  
Gerard BISERTE ◽  
Michel COHEN-SOLAL
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Amino Acid Sequences

scholarly journals Evidence for Nucleic Acid Binding Ability and Nucleosome Association of Bombyx mori Nucleopolyhedrovirus BRO Proteins

2000 ◽  
Vol 74 (15) ◽  
pp. 6784-6789 ◽  
Author(s):  
Evgueni A. Zemskov ◽  
WonKyung Kang ◽  
Susumu Maeda
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Bombyx Mori ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Amino Acid Sequences ◽  
Micrococcal Nuclease ◽  
Nucleic Acid Binding ◽  
Bombyx Mori Nucleopolyhedrovirus ◽  
Bmn Cells

ABSTRACT The Bombyx mori nucleopolyhedrovirus (BmNPV) genome contains five related members of the bro gene family, all of which are actively expressed in infected BmN cells. Although their functions are unknown, their amino acid sequences contain a motif found in all known viral and prokaryotic single-stranded DNA binding proteins. To determine if they bind to nucleic acids, we fractionated the nuclei of BmNPV-infected BmN cells using a histone extraction protocol. We detected BRO-A, BRO-C, and BRO-D in the histone H1 fraction using anti-BRO antibodies. Micrococcal nuclease treatment released these BRO proteins from the chromatin fraction, suggesting their involvement in nucleosome structures. Chromatographic fractionation showed that BRO-A and/or BRO-C interacted with core histones. Expression of partial sequences of BRO-A proved that the N-terminal 80 amino acid residues were required for DNA binding activity. We also demonstrated that BmNPV BRO proteins underwent phosphorylation and ubiquitination followed by proteasome degradation, which may explain their distribution in the cytoplasm as well as the nucleus. We propose that BRO-A and BRO-C may function as DNA binding proteins that influence host DNA replication and/or transcription.

scholarly journals Residues in the Swi5 Zinc Finger Protein That Mediate Cooperative DNA Binding with the Pho2 Homeodomain Protein

1998 ◽  
Vol 18 (11) ◽  
pp. 6436-6446 ◽  
Author(s):  
Leena T. Bhoite ◽  
David J. Stillman
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Zinc Finger ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Zinc Finger Protein ◽  
Interaction Analysis ◽  
Dna Binding Proteins ◽  
Two Hybrid

ABSTRACT The Swi5 zinc finger and the Pho2 homeodomain DNA-binding proteins bind cooperatively to the HO promoter.Pho2 (also known as Bas2 or Grf10) activates transcription of diverse genes, acting with multiple distinct DNA-binding proteins. We have performed a genetic screen to identify amino acid residues in Swi5 that are required for synergistic transcriptional activation of a reporter construct in vivo. Nine unique amino acid substitutions within a 24-amino-acid region of Swi5, upstream of the DNA-binding domain, reduce expression of promoters that require both Swi5 and Pho2 for activation. In vitro DNA binding experiments show that the mutant Swi5 proteins bind DNA normally, but some mutant Swi5 proteins (resulting from SWI5* mutations) show reduced cooperative DNA binding with Pho2. In vivo experiments show that these SWI5* mutations sharply reduce expression of promoters that require both SWI5 and PHO2, while expression of promoters that require SWI5 but arePHO2 independent is largely unaffected. This suggests that these SWI5* mutations do not affect the ability of Swi5 to bind DNA or activate transcription but specifically affect the region of Swi5 required for interaction with Pho2. Two-hybrid experiments show that amino acids 471 to 513 of Swi5 are necessary and sufficient for interaction with Pho2 and that the SWI5* point mutations cause a severe reduction in this two-hybrid interaction. Analysis of promoter activation by these mutants suggests that this small region of Swi5 has at least two distinct functions, conferring specificity for activation of the HO promoter and for interaction with Pho2.

Identify DNA-Binding Proteins with Optimal Chou’s Amino Acid Composition

2012 ◽  
Vol 19 (4) ◽  
pp. 398-405 ◽  
Author(s):  
Xiao-Wei Zhao ◽  
Xiang-Tao Li ◽  
Zhi-Qiang Ma ◽  
Ming-Hao Yin
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Binding Proteins ◽  
Dna Binding Proteins

Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding

1990 ◽  
Vol 23 (3) ◽  
pp. 205-280 ◽  
Author(s):  
Thomas A. Steitz
Keyword(s):  
Dna Binding ◽  
Crystal Structures ◽  
Binding Proteins ◽  
Regulatory Protein ◽  
Dna Binding Proteins ◽  
Structural Studies ◽  
Klenow Fragment ◽  
Proteolytic Fragment ◽  
Repressor Protein ◽  
E Coli

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, the E. coli catabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKay et al. 1982; Weber & Steitz, 1987), a cro repressor from phage λ (Anderson et al. 1981), and the DNA-binding proteolytic fragment of λcI repressor protein (Pabo & Lewis, 1982) Although crystallographic studies of the E. coli lac repressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitz et al. 1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure of λcro repressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP, λcro, λcI repressor fragment, 434 repressor fragment (Anderson et al. 1987), 434 cro repressor (Wolberger et al. 1988), E. coli trp repressor (Schevitz et al. 1985), E. coli met repressor (Rafferty et al. 1989)], EcoR I restriction endonuclease (McClarin et al. 1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfull et al. 1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment of E. coli DNA polymerase I (Ollis et al. 1985) and the E. coli Hu protein (Tanaka et al., 1984)].

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