B3 domain

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B3 DNA binding domain of RAV1
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The B3 DNA binding domain (DBD) is a highly conserved domain exclusively found in transcription factors from higher plants (≥40 species) (Pfam PF02362) combined with other domains (IPR003340). It consists of 100-120 residues, includes seven beta strands and two alpha helices which form a DNA-binding pseudobarrel protein fold (SCOP 117343); interacts with the major groove of DNA.[1]

Contents

[edit] B3 families

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

protein ARF1-B3 ABI3-B3 RAV1-B3
B3 structure derived by modelling[1] modelling[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.

[edit] 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]

[edit] See also

[edit] References

  1. ^ a b c d e 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 (2004). "Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1". Plant Cell 16 (12): 3448-59. doi:10.1105/tpc.104.026112. PMID 15548737. 
  2. ^ 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 (2000). "Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes". Science 290 (5499): 2105-10. doi:10.1126/science.290.5499.2105. PMID 11118137. 
  3. ^ Ulmasov T, Hagen G, Guilfoyle TJ (1997). "ARF1, a transcription factor that binds to auxin response elements". Science 276 (5320): 1865-8. PMID 9188533. 
  4. ^ Tiwari SB, Hagen G, Guilfoyle TJ (2003). "The roles of auxin response factor domains in auxin-responsive transcription". Plant Cell 15 (2): 533-43. PMID 12566590. 
  5. ^ Suzuki M, Kao CY, McCarty DR (1997). "The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity". Plant Cell 9 (5): 799-807. doi:10.1105/tpc.9.5.799. PMID 9165754. 
  6. ^ Ezcurra I, Wycliffe P, Nehlin L, Ellerström M, Rask L (2000). "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. PMID 11029704. 
  7. ^ Kagaya Y, Ohmiya K, Hattori T (1999). "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. PMID 9862967. 
  8. ^ Waltner, J.K., Peterson, F.C., Lytle, B.L., Volkman, B.F. (2005). "Structure of the B3 domain from Arabidopsis thaliana protein At1g16640". Protein Sci 14 (9): 2478-83. doi:10.1110/ps.051606305. PMID 16081658. 
  9. ^ Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L (2004). "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. doi:10.1016/j.jmb.2003.10.030. PMID 14659759. 
  10. ^ Grazulis S, Manakova E, Roessle M, Bochtler M, Tamulaitiene G, Huber R, Siksnys V (2005). "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. doi:10.1073/pnas.0507949102. PMID 16247004. 

[edit] External links

v • d • e
Transcription factors and intracellular receptors
(1) Basic domains
(1.1) Basic leucine zipper (bZIP)
Activating transcription factor (AATF, 1, 2, 3, 4, 5, 6, 7) • AP-1 (c-Fos, FOSB, FOSL1, FOSL2, c-Jun, JUNB, JUND) • BACH (1, 2) • BATF • BLZF1 • C/EBP (α, β, γ, δ, ε, ζ) • CREB (1, 3, L1) • CREM • DBP • DDIT3 • GABPA • HLF • MAF (B, F, G, K) • NFE (2, L1, L2) • NRL • NRF1 • XBP1
(1.2) Basic helix-loop-helix (bHLH)
ATOH1 • AhR • AHRR • ARNT • ASCL1 • BHLHB2 • BMAL (ARNTL, ARNTL2) • CLOCK • EPAS1 • HAND (1, 2) • HES (5, 6) • HEY (1, 2, L) • HES1 • HIF (1A, 3A) • ID (1, 2, 3, 4) • LYL1 • MXD4 • MYCL1 • MYCN • Myogenic regulatory factors (MyoD, Myogenin, MYF5, MYF6) • Neurogenins • NeuroD (1, 2) • NPAS (1, 2, 3) • OLIG (1, 2) • Scleraxis • TAL1 • Twist • USF1
(1.3) bHLH-ZIP
MAX • MITF • MNT • MLX • MXI1 • Myc • SREBP (1, 2)
(1.6) Basic helix-span-helix (bHSH)
(2) Zinc finger
DNA-binding domains
(2.1) Nuclear receptor (Cys4)
subfamily 1 (Thyroid hormone (α, β), CAR, FXR, LXR (α, β), PPAR (α, β/δ, γ), PXR, RAR (α, β, γ), ROR (α, β, γ), Rev-ErbA (α, β), VDR) • subfamily 2 (COUP-TF (I, II), Ear-2, HNF4 (α, γ), PNR, RXR (α, β, γ), Testicular receptor (2, 4), TLX) • subfamily 3 (Steroid hormone (Estrogen (α, β), Estrogen related (α, β, γ), Androgen, Glucocorticoid, Mineralocorticoid, Progesterone)) • subfamily 4 NUR (NGFIB, NOR1, NURR1) • subfamily 5 (LRH-1, SF1) • subfamily 6 (GCNF) • subfamily 0 (DAX1, SHP)
(2.2) Other Cys4
GATA (1, 2, 3, 4, 5, 6) • MTA (1, 2, 3)
(2.3) Cys2His2
ATBF1 • BCL(6, 11A, 11B) • CTCF • E4F1 • EGR (2, 3) • ERV3 • General transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF: 1, 2, TFIIH: 1, 2, 4, 2I, 3A, 3C1, 3C2) • GFI1 • GLI-Krüppel family (1, 2, 3, YY1) • HIC (1, 2) • HIVEP (1, 2, 3) • IKZF (1, 2, 3) • ILF (2, 3) • KLF (2, 4, 5, 6, 9, 10, 11, 12, 13) • MTF1 • MYT1 • OSR1 • Sp1 • zinc finger ((3, 7, 9, 10, 19, 22, 24, 33B, 34, 35, 41, 43, 44, 51, 74, 143, 146, 148, 165, 202, 217, 219, 238, 239, 259, 267, 268, 281, 295, 318, 330, 346, 350, 365, 366, 384, 451, 452, 471, 593, 638, 649, 655) • Zbtb7 (7A) • ZBT (16, 17, 33)
(2.4) Cys6
(2.5) Alternating composition
AIRE • DIDO1 • GRLF1 • ING (1, 2, 4) • JARID (1A, 1B, 1C, 1D, 2) • JMJD1B
(3) Helix-turn-helix
domains
ARX • CDX (1, 2) • CRX • CUTL1 • DLX (3, 4, 5) • EMX2 • EN (1, 2) • FHL (1, 2, 3) • HESX1 • HHEX • HLX • Homeobox (A1, A3, A4, A5, A7, A9, A10, A11, A13, B1, B2, B3, B4, B5, B6, B7, B8, B9, B13, C4, C5, C6, C8, C9, C10, C11, C13, D1, D3, D4, D8, D9, D10, D11, D12, D13) • HOPX • MEIS (1, 2) • MEOX2 • MNX1 • MSX (1, 2) • NANOG • NKX (2-1, 2-5, 3-1) • PHF (3, 6, 10, 17) • POU domain (PIT-1, BRN-3: 1, 2, Octamer transcription factor: 1, 2, 3/4, 6, 7) • OTX (1, 2) • PDX1
(3.2) Paired box
PAX (1, 2, 3, 4, 5, 6, 7, 8, 9)
E2F (1, 2, 3, 4, 5) • FOX proteins (C1, C2, E1, G1, H1, K2, L2, M1, N3, O1A, , O3A, O4, P1, P2, P3)
HSF (1, 2, 4)
(3.5) Tryptophan clusters
ELF (4, 5) • EGF • ELK (1, 3, 4) • ERF • ERG • ETS (1, 2) • ETV (1, 4, 5, 6) • FLI1 • Interferon regulatory factors (1, 2, 3, 4, 5, 6, 7, 8) • MYB • MYBL2
(3.6) TEA domain
transcriptional enhancer factor 1, 2
(4) β-Scaffold factors with
minor groove contacts
(4.1) Rel homology region
NF-κB (NFKB1, NFKB2, REL, RELA, RELB) • NFAT (C1, C2, C3, C4, 5)
(4.2) STAT
STAT (1, 2, 3, 4, 5, 6)
(4.3) p53
(4.4) MADS box
Mef2 (A, B, C, D) • SRF
HNF (1A, 1B) • LEF1 • SOX (2, 3, 4, 5, 6, 8, 9, 10, 11, 13, 15, 18) • SRY • SSRP1
(4.10) Cold-shock domain
(4.11) Runt
(0) Other
transcription factors
(0.2) HMGI(Y)
HMGA (1, 2) • HBP1
Rb • RBL1 • RBL2
(0.5) AP-2/EREBP-related factors
Apetala 2 • EREBP • B3
(0.6) Miscellaneous
ARID (1A, 1B, 2, 3A, 3B, 4A) • CAP • IFI (16, 35) • MLL (2, 3, T1) • MNDA • NFI (A, B, C, X) • NFY (A, B, C) • Rho/Sigma • R-SMAD