DNA-binding domain
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A DNA-binding domain (DBD) includes any protein motif that binds to double- or single-stranded DNA with affinity to a specific sequence or set thereof or a general affinity to DNA.[1]
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[edit] Function
DNA-binding domains are included in many proteins involved in the regulation of gene expression (including transcription factors), proteins involved in the packaging of DNA within the nucleus (such as histones), nucleic acid dependent-polymerases involved in DNA replication and transcription, or any of many accessory proteins which are involved in these processes.
Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair.
The specificity of DNA-binding proteins can be identified using a technique called "DNA Footprinting".
[edit] Types of DNA-binding domains
[edit] Helix-turn-helix
Originally discovered in bacteria, this motif is commonly found in repressor proteins and is about 20 amino acids long. In eukaryotes, the homeodomain comprises 3 helices, of which the third recognizes the DNA (aka recognition helix). They are common in proteins that regulate developmental processes.
[edit] Zinc finger
This domain is 30 amino acids long and consists of a recognition helix and a 2-strand beta-sheet. The domain also contains four regularly spaced ligands for Zinc (either histidines or cysteines). The Zn ion stabilizes the 3D structure of the domain. Each finger contains one Zn ion and recognizes a specific triplet of DNA basepairs.
[edit] Leucine zipper
The basic leucine zipper (bZIP) domain contains an alpha helix with a leucine at every 7th amino acid. If two such helices find one another, the leucines can interact as the teeth in a zipper, allowing dimerization of two proteins. When binding to the DNA, basic amino acid residues bind to the sugar-phosphate backbone while the helices sit in the major grooves.
[edit] Winged helix
Consisting of about 110 amino acids, the winged helix (WH) domain has four helices and a two-strand beta-sheet.
[edit] Winged helix turn helix
The winged helix turn helix domain (wHTH) SCOP 46785 is typically 85-90 amino acids long. It is formed by a 3-helical bundle and a 4-strand beta-sheet (wing).
[edit] Helix-loop-helix
This domain is found in some transcription factors and is characterized by two α helices connected by a loop. One helix is typically smaller and due to the flexibility of the loop, allows dimerization by folding and packing against another helix. The larger helix typically contains the DNA binding regions.
[edit] Unusual DNA binding domains
[edit] Immunoglobulin fold
The domain (IPR013783) consists of a beta-sheet structure with large connecting loops, which serve to recognize either DNA major grooves or antigens. Usually found in immunoglobulin proteins, they are also present in Stat proteins of the cytokine pathway. This is likely because the cytokine pathway evolved relatively recently and has made use of systems that were already functional, rather than creating its own.
[edit] B3 domain
The B3 DBD (IPR003340, SCOP 117343) is found exclusively in transcription factors from higher plants and consists of 100-120 residues. It includes seven beta sheets and two alpha helices which form a DNA-binding pseudobarrel protein fold.
[edit] References
- ^ Lilley, David M. J. (1995). DNA-protein: structural interactions. Oxford: IRL Press at Oxford University Press. ISBN 0-19-963453-X.
[edit] External links
- DBD database of predicted transcription factors[1] Uses a curated set of DNA-binding domains to predict transcription factors in all completely sequenced genomes
- Table of DNA-binding motifs
- MeSH DNA+Footprinting
- MeSH DNA-Binding+Proteins
