Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Nov;21(11):3416-20.
doi: 10.1105/tpc.109.069088. Epub 2009 Nov 17.

The Arabidopsis B-box zinc finger family

Rajnish Khanna, Brent Kronmiller, Don R Maszle, George Coupland, Magnus Holm, Takeshi Mizuno, Shu-Hsing Wu

The Arabidopsis B-box zinc finger family

Rajnish Khanna et al. Plant Cell. 2009 Nov.
No abstract available

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
The B-Box Family of Proteins from Arabidopsis Have Two Distinct B-Box Domains. Motif logos (Schneider and Stephens, 1990; Crooks et al., 2004) of protein alignments of B-box B1 (A) and B2 (B) show differences. Conservation of residues across all proteins is shown by height of each letter; a position with all like residues has a bit score of 4. The 38 conserved residues of B1 and B2 are shown; see Table 1 for individual coordinates of each B-box motif. B1 is more conserved, containing 12 out of 38 residues that are seen in 95% of the 32 family members. B2 shows seven amino acids with 95% conservation. The conserved residues of B2 are also found conserved in B1.
Figure 2.
Figure 2.
Phylogenetic Analysis of the Arabidopsis B-Box Family. Full-length proteins of the 32 B-box members were aligned using MUSCLE (maxiters = 16) (Edgar, 2004). Multiple alignments were viewed and realigned using SeaView (Galtier et al., 1996). MrBayes (Huelsenbeck and Ronquist, 2001) was used to construct a Bayesian inference phylogenetic tree with 1,000,000 generations. Bayesian posterior probability values are displayed on the tree as percentages, and if differing values were seen between the two independently run trees, both are displayed. This phylogeny was used to order B-box genes to provide a uniform naming terminology. For full-length protein sequences used and the multiple alignments, see Supplemental Data Set 1 (FASTA format) and Supplemental Figure 1 (alignment) online.
Figure 3.
Figure 3.
Structure Classification of the B-Box Family. A graphical representation of a phylogeny is shown at left with Arabidopsis Genome Initiative gene names. Schematics of identified protein structures are shown; B-box 1 is labeled as B1, B-box 2 is labeled as B2, and the CCT domain is indicated. Following the structure of each protein is the new BBX naming scheme, synonym/s for proteins, and structure groups. References: 1Koornneef et al. (1991), 2Putterill et al. (1995), 3Robson et al. (2001), 4Kumagai et al. (2008), 5Datta et al. (2007), 6Datta et al. (2008), 7Chang et al. (2008), 8Holm et al. (2001), and 9Datta et al. (2006).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 3389–3402. - PMC - PubMed
    1. Bailey, P.C., Martin, C., Toledo-Ortiz, G., Quail, P.H., Huq, E., Heim, M.A., Jakoby, M., Werber, M., and Weisshaar, B. (2003). Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell 15 2497–2502. - PMC - PubMed
    1. Borden, K.L., Lally, J.M., Martin, S.R., O'Reilly, N.J., Etkin, L.D., and Freemont, P.S. (1995). Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development. EMBO J. 14 5947–5956. - PMC - PubMed
    1. Briggs, W.R., et al. (2001). The phototropin family of photoreceptors. Plant Cell 13 993–997. - PMC - PubMed
    1. Chang, C.S., Li, Y.H., Chen, L.-T., Chen, W.-C., Hsieh, W.-P., Shin, J., Jane, W.-N., Chou, S.-J., Choi, G., Hu, J.-M., Somerville, S., and Wu, S.-H. (2008). LZF1, a HY5-regulated transcriptional factor, functions in Arabidopsis de-etiolation. Plant J. 54 205–219. - PubMed

MeSH terms