B3 domain
Encyclopedia
The B3 DNA binding domain (DBD) is a highly conserved domain
found exclusively in transcription factor
s, from higher plants (≥40 species) combined with other domains . It consists of 100-120 residues, includes seven beta strands
and two alpha helices
that form a DNA-binding pseudobarrel protein fold
; it interacts with the major groove of DNA.
, there are three main families of transcription factors that contain B3 domain:
and are only known NMR
solution phase structures of the B3 DNA Binding Domain.
.
DNA-binding domain
A DNA-binding domain is an independently folded protein domain that contains at least one motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence or have a general affinity to DNA...
found exclusively in transcription factor
Transcription factor
In molecular biology and genetics, a transcription factor is a protein that binds to specific DNA sequences, thereby controlling the flow of genetic information from DNA to mRNA...
s, from higher plants (≥40 species) combined with other domains . It consists of 100-120 residues, includes seven beta strands
Beta sheet
The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...
and two alpha helices
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
that form a DNA-binding pseudobarrel protein fold
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
; it interacts with the major groove of DNA.
B3 families
In Arabidopsis thalianaArabidopsis thaliana
Arabidopsis thaliana is a small flowering plant native to Europe, Asia, and northwestern Africa. A spring annual with a relatively short life cycle, arabidopsis is popular as a model organism in plant biology and genetics...
, there are three main families of transcription factors that contain B3 domain:
- ARF (AuxinAuxinAuxins are a class of plant hormones with some morphogen-like characteristics. Auxins have a cardinal role in coordination of many growth and behavioral processes in the plant's life cycle and are essential for plant body development. Auxins and their role in plant growth were first described by...
Respose Factors) - ABI3 (ABscisic acidAbscisic acidAbscisic acid , also known as abscisin II and dormin, is a plant hormone. ABA functions in many plant developmental processes, including bud dormancy. It is degraded by the enzyme -abscisic acid 8'-hydroxylase.-Function:...
Insensitive3) - RAV (Related to ABI3/VP1)
| protein | ARF1-B3 | ABI3-B3 | RAV1-B3 |
|---|---|---|---|
| B3 structure derived by | molecular model Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... |
molecular model Molecular modelling Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small... |
NMR Protein nuclear magnetic resonance spectroscopy Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by Richard R. Ernst and Kurt Wüthrich, among others... |
| B3 recognition sequence Recognition sequence The recognition sequence, sometimes also referred to as recognition site, of any DNA-binding protein motif that exhibits binding specificity, refers to the DNA sequence , to which the domain is specific... |
TGTCTC | CATGCA | CACCTG |
and are only known NMR
Protein nuclear magnetic resonance spectroscopy
Nuclear magnetic resonance spectroscopy of proteins is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins. The field was pioneered by Richard R. Ernst and Kurt Wüthrich, among others...
solution phase structures of the B3 DNA Binding Domain.
Related proteins
The N-terminal domain of restriction endonuclease EcoRII; the C-terminal domain of restriction endonuclease BfiI possess a similar DNA-binding pseudobarrel protein foldTertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
.
External links
- DBD database of predicted transcription factors Uses a curated set of DNA-binding domains to predict transcription factors in all completely sequenced genomes
- Classification in the "Transcription factors" table according to the Transfac database.
- Database of Arabidopsis Transcription Factors