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 genera ...
(DBD) is a
highly conserved domain 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 of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The f ...
s (≥40 species) () combined with other domains (). It consists of 100-120 residues, includes seven
beta strands
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labio ...
and two
alpha helices
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...
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 similari ...
(); it interacts with the major groove of
DNA.
B3 families
In ''
Arabidopsis thaliana'', 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 nuclei in a strong constant magnetic field are perturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with ...
solution phase structures of the B3 DNA Binding Domain.
Related proteins
The
N-terminal 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
Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in ''Escherichia coli'', a Gram-negative bacteria. Its molecular mass is 45.2 Atomic mass unit, kDa, being compos ...
; the
C-terminal
The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal 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 the protein is ...
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 similari ...
.
See also
*Restriction endonuclease
EcoRII
Restriction endonuclease (REase) EcoRII (pronounced "eco R two") is an enzyme of restriction modification system (RM) naturally found in ''Escherichia coli'', a Gram-negative bacteria. Its molecular mass is 45.2 Atomic mass unit, kDa, being compos ...
*
Auxin
*
Abscisic acid
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