scholarly journals The structure of the Thermococcus gammatolerans McrB N-terminal domain reveals a new mode of substrate recognition and specificity among McrB homologs

2019 ◽  
Vol 295 (3) ◽  
pp. 743-756 ◽  
Author(s):  
Christopher J. Hosford ◽  
Anthony Q. Bui ◽  
Joshua S. Chappie
Keyword(s):  
Dna Binding ◽  
Mutational Analysis ◽  
Binding Pocket ◽  
Binding Mode ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Modified Dna ◽  
Structural Superposition ◽  
Aromatic Cage ◽  
Preferential Binding

McrBC is a two-component, modification-dependent restriction system that cleaves foreign DNA-containing methylated cytosines. Previous crystallographic studies have shown that Escherichia coli McrB uses a base-flipping mechanism to recognize these modified substrates with high affinity. The side chains stabilizing both the flipped base and the distorted duplex are poorly conserved among McrB homologs, suggesting that other mechanisms may exist for binding modified DNA. Here we present the structures of the Thermococcus gammatolerans McrB DNA-binding domain (TgΔ185) both alone and in complex with a methylated DNA substrate at 1.68 and 2.27 Å resolution, respectively. The structures reveal that TgΔ185 consists of a YT521-B homology (YTH) domain, which is commonly found in eukaryotic proteins that bind methylated RNA and is structurally unrelated to the E. coli McrB DNA-binding domain. Structural superposition and co-crystallization further show that TgΔ185 shares a conserved aromatic cage with other YTH domains, which forms the binding pocket for a flipped-out base. Mutational analysis of this aromatic cage supports its role in conferring specificity for the methylated adenines, whereas an extended basic surface present in TgΔ185 facilitates its preferential binding to duplex DNA rather than RNA. Together, these findings establish a new binding mode and specificity among McrB homologs and expand the biological roles of YTH domains.

scholarly journals Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)

2014 ◽  
Vol 42 (9) ◽  
pp. 5937-5948 ◽  
Author(s):  
Doyoun Kim ◽  
Jeonghwan Hur ◽  
Kwangsoo Park ◽  
Sangsu Bae ◽  
Donghyuk Shin ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Dna Binding ◽  
Binding Mode ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Z Dna

scholarly journals Mutational analysis of the DNA binding domain A of chromosomal protein HMG1

1994 ◽  
Vol 22 (3) ◽  
pp. 285-292 ◽  
Author(s):  
Luca Falciola ◽  
Alastair I.H. Murchie ◽  
David M.J. Lilley ◽  
Marco E. Bianchi
Keyword(s):  
Dna Binding ◽  
Mutational Analysis ◽  
Binding Domain ◽  
Chromosomal Protein ◽  
Dna Binding Domain

scholarly journals Mutational Analysis of Conserved Residues in the Putative DNA-Binding Domain of the Response Regulator Spo0A ofBacillus subtilis

2000 ◽  
Vol 182 (24) ◽  
pp. 6975-6982 ◽  
Author(s):  
Janet K. Hatt ◽  
Philip Youngman
Keyword(s):  
Dna Binding ◽  
Transcriptional Activation ◽  
Mutational Analysis ◽  
Response Regulator ◽  
Gene Activation ◽  
Binding Domain ◽  
Site Directed Mutagenesis ◽  
Specific Gene ◽  
Dna Binding Domain ◽  
Conserved Residues

ABSTRACT The Spo0A protein of Bacillus subtilis is a DNA-binding protein that is required for the expression of genes involved in the initiation of sporulation. Spo0A binds directly to and both activates and represses transcription from the promoters of several genes required during the onset of endospore formation. The C-terminal 113 residues are known to contain the DNA-binding activity of Spo0A. Previous studies identified a region of the C-terminal half of Spo0A that is highly conserved among species of endospore-formingBacillus and Clostridium and which encodes a putative helix-turn-helix DNA-binding domain. To test the functional significance of this region and determine if this motif is involved in DNA binding, we changed three conserved residues, S210, E213, and R214, to Gly and/or Ala by site-directed mutagenesis. We then isolated and analyzed the five substitution-containing Spo0A proteins for DNA binding and sporulation-specific gene activation. The S210A Spo0A mutant exhibited no change from wild-type binding, although it was defective in spoIIA and spoIIE promoter activation. In contrast, both the E213G and E213A Spo0A variants showed decreased binding and completely abolished transcriptional activation of spoIIA and spoIIE, while the R214G and R214A variants completely abolished both DNA binding and transcriptional activation. These data suggest that these conserved residues are important for transcriptional activation and that the E213 residue is involved in DNA binding.

scholarly journals Mutational analysis of the DNA-binding domain of the CYS3 regulatory protein of Neurospora crassa.

1991 ◽  
Vol 11 (9) ◽  
pp. 4356-4362 ◽  
Author(s):  
M N Kanaan ◽  
G A Marzluf
Keyword(s):  
Dna Binding ◽  
Neurospora Crassa ◽  
Mutational Analysis ◽  
Regulatory Gene ◽  
Regulatory Protein ◽  
Binding Activity ◽  
Binding Domain ◽  
Site Directed Mutagenesis ◽  
Dna Binding Domain ◽  
Dna Binding Activity

cys-3, the major sulfur regulatory gene of Neurospora crassa, activates the expression of a set of unlinked structural genes which encode sulfur catabolic-related enzymes during conditions of sulfur limitation. The cys-3 gene encodes a regulatory protein of 236 amino acid residues with a leucine zipper and an upstream basic region (the b-zip region) which together may constitute a DNA-binding domain. The b-zip region was expressed in Escherichia coli to examine its DNA-binding activity. The b-zip domain protein binds to the promoter region of the cys-3 gene itself and of cys-14, the sulfate permease II structural gene. A series of CYS3 mutant proteins obtained by site-directed mutagenesis were expressed and tested for function, dimer formation, and DNA-binding activity. The results demonstrate that the b-zip region of cys-3 is critical for both its function in vivo and specific DNA-binding in vitro.

scholarly journals Characterization of the DNA-Binding Domain of the Avian Y-Box Protein, chkYB-2, and Mutational Analysis of Its Single-Strand Binding Motif in the Rous Sarcoma Virus Enhancer

1998 ◽  
Vol 72 (2) ◽  
pp. 900-909 ◽  
Author(s):  
Ashok Nambiar ◽  
S. K. Swamynathan ◽  
Jagannadha C. Kandala ◽  
Ramareddy V. Guntaka
Keyword(s):  
Dna Binding ◽  
Rous Sarcoma Virus ◽  
Mutational Analysis ◽  
Binding Domain ◽  
Single Strand ◽  
Dna Binding Domain ◽  
Single Stranded Dna ◽  
High Affinity ◽  
Rous Sarcoma ◽  
Sarcoma Virus

ABSTRACT chkYB-2 is a sequence-specific, single-stranded DNA binding chicken Y-box protein that promotes Rous sarcoma virus long terminal repeat (RSV LTR)-driven transcription in avian fibroblasts. The DNA-binding domain of chkYB-2 has been mapped by characterizing the DNA binding properties of purified recombinant chkYB-2 mutant polypeptides. The data indicate that the invariant cold shock domain (CSD) is necessary but not sufficient for association with DNA and suggest that another conserved region, adjacent to the carboxyl boundary of the CSD, plays a role in high-affinity DNA binding. chkYB-2 binds to a tandem repeat of the 5′-GTACCACC-3′ motif on the RSV LTR. Mutational analysis of this recognition sequence revealed the requirement of an essentially unaltered template for both high-affinity binding by chkYB-2 as well as maximal transcriptional activity of the RSV LTR in vivo. The single-stranded DNA binding activity of chkYB-2 is augmented by Mg2+. The possible significance of this finding for transactivation by a single-strand DNA binding protein is discussed.

scholarly journals Systematic mutational analysis of the LytTR DNA binding domain of Staphylococcus aureus virulence gene transcription factor AgrA

2014 ◽  
Vol 42 (20) ◽  
pp. 12523-12536 ◽  
Author(s):  
Sophie S. Nicod ◽  
Robert O. J. Weinzierl ◽  
Lynn Burchell ◽  
Andres Escalera-Maurer ◽  
Ellen H. James ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Transcription Factor ◽  
Dna Binding ◽  
Gene Transcription ◽  
Mutational Analysis ◽  
Virulence Gene ◽  
Binding Domain ◽  
Dna Binding Domain
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