B3 domain explained

Symbol:	B3_domain
B3 DNA binding domain
Pfam:	PF02362
Interpro:	IPR003340
Prosite:	PS50863
Scop:	1wid
Cdd:	cd10017
Pdb:	,

The B3 DNA binding domain (DBD) is a highly conserved domain found exclusively in transcription factors (≥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.

B3 families

In Arabidopsis thaliana, there are three main families of transcription factors that contain B3 domain:^[1]

• 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	molecular model	NMR
	TGTCTC^[2] ^[3]	CATGCA^[4] ^[5]	CACCTG^[6]

^[7] and ^[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

External links

• DBD database of predicted transcription factors Kummerfeld SK, Teichmann SA . DBD: a transcription factor prediction database . Nucleic Acids Res. . 34 . Database issue . D74–81 . 2006 . 16381970 . 10.1093/nar/gkj131 . 1347493. 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
• B3, RAV, and ARF family at PlantTFDB:Plant Transcription Factor Database

Notes and References

1. Riechmann JL, Heard J, Martin G, Reuber L, Jiang C, Keddie J, Adam L, Pineda O, Ratcliffe OJ, Samaha RR, Creelman R, Pilgrim M, Broun P, Zhang JZ, Ghandehari D, Sherman BK, Yu G . Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes . Science . 290 . 5499 . 2105–10 . 2000 . 11118137 . 10.1126/science.290.5499.2105 . 2000Sci...290.2105R .
2. Ulmasov T, Hagen G, Guilfoyle TJ . ARF1, a transcription factor that binds to auxin response elements . Science . 276 . 5320 . 1865–8 . 1997 . 9188533 . 10.1126/science.276.5320.1865.
3. Tiwari SB, Hagen G, Guilfoyle TJ . The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription . Plant Cell . 15 . 2 . 533–43 . 2003 . 12566590 . 10.1105/tpc.008417 . 141219.
4. Suzuki M, Kao CY, McCarty DR . The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity . Plant Cell . 9 . 5 . 799–807 . 1997 . 9165754 . 10.1105/tpc.9.5.799 . 156957.
5. Ezcurra I, Wycliffe P, Nehlin L, Ellerström M, Rask L . Transactivation of the Brassica napus napin promoter by ABI3 requires interaction of the conserved B2 and B3 domains of ABI3 with different cis-elements: B2 mediates activation through an ABRE, whereas B3 interacts with an RY/G-box . Plant J. . 24 . 1 . 57–66 . 2000 . 11029704 . 10.1046/j.1365-313x.2000.00857.x.
6. Kagaya Y, Ohmiya K, Hattori T . RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants . Nucleic Acids Res. . 27 . 2 . 470–8 . 1999 . 9862967 . 10.1093/nar/27.2.470 . 148202.
7. Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Tomo Y, Hayami N, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S . Solution Structure of the B3 DNA Binding Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1 . Plant Cell . 16 . 12 . 3448–59 . 2004 . 15548737 . 10.1105/tpc.104.026112. 535885 .
8. Waltner, J.K. . Peterson, F.C. . Lytle, B.L. . Volkman, B.F. . Structure of the B3 domain from Arabidopsis thaliana protein At1g16640 . Protein Sci . 14 . 9 . 2478–83 . 2005 . 16081658 . 10.1110/ps.051606305 . 2253459 .
9. Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L . Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold . J. Mol. Biol. . 335 . 1 . 307–19 . 2004 . 14659759 . 10.1016/j.jmb.2003.10.030 .
10. Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V . Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease . Proc. Natl. Acad. Sci. U.S.A. . 102 . 44 . 15797–802 . 2005 . 16247004 . 10.1073/pnas.0507949102. 1266039 . 2005PNAS..10215797G . free .