The B3
DNA binding domain
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 ...
(DBD) is a
highly conserved domain
A domain is a geographic area controlled by a single person or organization. Domain may also refer to:
Law and human geography
* Demesne, in English common law and other Medieval European contexts, lands directly managed by their holder rather ...
found exclusively in
transcription factor
In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription (genetics), transcription of genetics, genetic information from DNA to messenger RNA, by binding t ...
s (≥40 species) () combined with other domains (). It consists of 100-120 residues, includes seven
beta strands and two
alpha helices
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix).
The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of l ...
that form a DNA-binding pseudobarrel
protein fold
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similar ...
(); it interacts with the major groove of
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
.
B3 families
In ''
Arabidopsis thaliana
''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. Commonly found along the shoulders of roads and in disturbed land, it is generally ...
'', there are three main families of transcription factors that contain B3 domain:
* ARF (
Auxin Response Factors)
* ABI3 (
ABscisic acid Insensitive3)
* RAV (Related to ABI3/VP1)
and
are only known
NMR
Nuclear magnetic resonance (NMR) is a physical phenomenon in which atomic nucleus, nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near and far field, near field) and respond by producing ...
solution phase structures of the B3 DNA Binding Domain.
Related proteins
The
N-terminal
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amin ...
domain of
restriction endonuclease
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
EcoRII
EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in ''Escherichia coli'', a Gram-negative bacteria. Its molecular mass is 45.2 Atomic mass unit, kDa, being co ...
; the
C-terminal
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal tail, carboxy tail, C-terminal end, or COOH-terminus) is the end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group (-COOH). When t ...
domain of
restriction endonuclease
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
BfiI possess a similar DNA-binding pseudobarrel
protein fold
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similar ...
.
See also
*Restriction endonuclease
EcoRII
EcoRII (pronounced 'eco R two') is an Restriction endonuclease enzyme (REase) of the restriction modification system (RM) naturally found in ''Escherichia coli'', a Gram-negative bacteria. Its molecular mass is 45.2 Atomic mass unit, kDa, being co ...
*
Auxin
Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essent ...
*
Abscisic acid
Abscisic acid (ABA or abscisin II) is a plant hormone. ABA functions in many plant developmental processes, including seed and bud dormancy, the control of organ size and stomatal closure. It is especially important for plants in the response to ...
References
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 th
database.
Database of Arabidopsis Transcription FactorsB3
RAV
an
ARF
family a
PlantTFDB:Plant Transcription Factor Database
{{Transcription factors, g0
Molecular genetics
Gene expression
Transcription factors
Protein domains