scholarly journals Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaoyuan He ◽  
Liqin Wang ◽  
Shuishu Wang
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Sequence ◽  
Response Regulator ◽  
Structural Basis ◽  
Sequence Recognition ◽  
Dna Sequence Recognition

scholarly journals The structural basis of differential DNA sequence recognition by restriction–modification controller proteins

2012 ◽  
Vol 40 (20) ◽  
pp. 10532-10542 ◽  
Author(s):  
N. J. Ball ◽  
J. E. McGeehan ◽  
S. D. Streeter ◽  
S.-J. Thresh ◽  
G. G. Kneale
Keyword(s):  
Dna Sequence ◽  
Structural Basis ◽  
Sequence Recognition ◽  
Restriction Modification ◽  
Dna Sequence Recognition

scholarly journals Structural basis of DNA sequence recognition by the response regulator PhoP

2014 ◽  
Vol 70 (a1) ◽  
pp. C1409-C1409
Author(s):  
Xiaoyuan He ◽  
Shuishu Wang
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Dna Sequence ◽  
Response Regulator ◽  
Direct Repeat ◽  
Regulatory Domain ◽  
Response Regulators ◽  
Sequence Recognition ◽  
Repeat Dna ◽  
Dna Sequence Recognition

The PhoP-PhoR two-component system plays a key role in regulating virulence of Mycobacterium tuberculosis. The response regulator PhoP is a transcription regulator, and it regulates expression of more than 100 genes. PhoP belongs to the OmpR/PhoB subfamily of response regulators. Despite extensive research in recent years, the molecular mechanism of DNA sequence recognition by this large subfamily of response regulators is not fully understood, especially the role of the N-terminal regulatory domain on DNA binding of the effector domain. Here we present a crystal structure of the full-length PhoP in complex with a direct-repeat DNA sequence. PhoP binds to DNA as a dimer. The two effector domains bind in tandem, each interacting with a half site of the direct repeat DNA. The DNA recognition helix inserts into the major groove, reading the sequence of a 7-bp motif. The wing residues interact with the downstream sequence, with a conserved arginine side chain inserting into the minor groove. Surprisingly, the regulatory domain also forms a tandem arrangement, instead of the anticipated symmetric dimer. The regulatory domain of the upstream protomer interacts with both domains of the downstream protomer. The structural elements of the alpha4-beta5-alpha5 face, which often found to be involved in dimer interface of the regulatory domain, play important roles in the interactions between the protomers. The crystal structure explains why PhoP recognizes direct repeats of two 7-bp motifs with a strict spacing of 4 bp and the highly cooperative binding of the two monomers. Detailed analysis of the structure along with analysis of the DNA sequence requirements and ITC measurements of protein-DNA binding interactions will be presented.

Creation of a Synthetic Ligand for Mitochondrial DNA Sequence Recognition and Promoter-Specific Transcription Suppression

2017 ◽  
Vol 139 (25) ◽  
pp. 8444-8447 ◽  
Author(s):  
Takuya Hidaka ◽  
Ganesh N. Pandian ◽  
Junichi Taniguchi ◽  
Tomohiro Nobeyama ◽  
Kaori Hashiya ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Sequence Recognition ◽  
Mitochondrial Dna Sequence ◽  
Synthetic Ligand ◽  
Transcription Suppression ◽  
Dna Sequence Recognition

MuA Transposase Separates DNA Sequence Recognition from Catalysis†

Biochemistry ◽  
2003 ◽  
Vol 42 (49) ◽  
pp. 14633-14642 ◽  
Author(s):  
Ilana Goldhaber-Gordon ◽  
Michael H. Early ◽  
Tania A. Baker
Keyword(s):  
Dna Sequence ◽  
Sequence Recognition ◽  
Dna Sequence Recognition
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