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A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication protein A is the best-understood member of this family and is used in processes where the double helix is separated, including DNA replication, recombination and DNA repair. [18]
A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA.A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA. [1]
Histone-like proteins are present in many Eubacteria, Cyanobacteria, and Archaebacteria.These proteins participate in all DNA-dependent functions; in these processes, bacterial DNA binding proteins have an architectural role, maintaining structural integrity as transcription, recombination, replication, or any other DNA-dependent process proceeds.
[1] [2] Some proteins will rearrange the layout of nucleosomes along the DNA in order to expose the promoter site (ATP-dependent chromatin remodeling complexes). [1] [2] Other proteins affect the binding between histones and DNA via post-translational histone modifications, allowing the DNA tightly wrapped into nucleosomes to loosen. [1] [2]
Single-strand DNA-binding protein (SSB) is a protein found in Escherichia coli (E. coli) bacteria, that binds to single-stranded regions of deoxyribonucleic acid (). [1] Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair.
DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known as transcription factors , and are thus linked to transcriptional regulation .
As an example, the Enterobacterial proteins have nearly identical N- and C-terminal sequences, however they are characterized by numerous amino acid adjustments, elisions, and insertions in the variable regions. [17] There is an AAA+ family ATPase motif and an independent DNA binding sphere in the C-terminal region.
Cryo-EM structure of the DNA-bound PolD–PCNA processive complex Structural basis for DNA binding by the PolD–PCNA complex. A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds ...