Pfam 22.0 :: B3
Description of the B3 family
B2-adapt-app_C <-- --> B3_4

B3


Accession number: PF02362
B3 DNA binding domain

This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in [1] this domain is found in VP1/AB13 transcription factors [2]. Some proteins also have a second AP2 DNA binding domain AP2 such as RAV1 Q9ZWM9 [1]. DNA binding activity was demonstrated by [3].

Description

Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors PUBMED:9862967. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations PUBMED:9862967.
Description text from InterPro entry IPR003340

Sequence information


Alignment

Seed (160)  Full (535)
Format:

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Species distribution

Tree depth:

Literature References

[1]
RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants.
Kagaya Y, Ohmiya K, Hattori T;
Nucleic Acids Res 1999;27:470-478.
[2]
ARF1, a transcription factor that binds to auxin response elements.
Ulmasov T, Hagen G, Guilfoyle TJ;
Science 1997;276:1865-1868.
[3]
The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity.
Suzuki M, Kao CY, McCarty DR;
Plant Cell 1997;9:799-807.

Database References

PFAMB
The following Pfam-B families contain sequences that according to Prodom are members of this Pfam-A family.
PB107491 PB128078 PB150376 PB151485 PB175575 PB176471 PB177292 PB179488 PB181550
INTERPRO IPR003340

HMMER build information

Pfam_ls [download HMM] Pfam_fs [download HMM]
Gathering cutoff 26.50 26.50 23.00 23.00
Trusted cutoff 26.90 26.90 23.50 23.40
Noise cutoff 25.90 26.30 22.90 22.90
Build method of HMM hmmbuild -F HMM_ls SEED
hmmcalibrate --seed 0 HMM_ls
 hmmbuild -f -F HMM_fs SEED
hmmcalibrate --seed 0 HMM_fs

Pfam specific information

Author of entryBashton M, Bateman A
Type definitionFamily
Source of seed membersPfam-B_582 (release 5.2)