B3 domain

The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors (≥40 species) (Pfam PF02362) combined with other domains (InterPro: IPR003340). It consists of 100-120 residues, includes seven beta strands and two alpha helices that form a DNA-binding pseudobarrel protein fold (SCOP 117343); it interacts with the major groove of DNA.^[1]

B3 DNA binding domain
B3 DNA binding domain of RAV1
Identifiers
Symbol	B3_domain
Pfam	PF02362
InterPro	IPR003340
PROSITE	PS50863
SCOP2	1wid / SCOPe / SUPFAM
CDD	cd10017
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary PDB 1wid​, 1yel​

B3 families

In Arabidopsis thaliana, there are three main families of transcription factors that contain B3 domain:^[2]

• ARF (Auxin Response Factors)
• ABI3 (ABscisic acid Insensitive3)
• RAV (Related to ABI3/VP1)

protein	ARF1-B3	ABI3-B3	RAV1-B3
B3 structure derived by	molecular model[1]	molecular model[1]	NMR[1]
B3 recognition sequence	TGTCTC[3][4]	CATGCA[5][6]	CACCTG[7]

PDB: 1WID​^[1] and PDB: 1YEL​^[8] are only known NMR 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 fold.^[9][10]

See also

• Restriction endonuclease EcoRII
• Auxin
• Abscisic acid