B3結構域

維基百科，自由的百科全書
B3 DNA binding domain
RAV1的B3 DNA結合結構域
鑑定
標誌B3_domain
PfamPF02362（舊版）
InterPro（英語：InterPro）IPR003340
PROSITE（英語：PROSITE）PS50863
SCOP（英語：Structural Classification of Proteins）1wid / SUPFAM
CDD（英語：Conserved Domain Database）cd10017

B3 DNA結合結構域（英語：B3 DNA binding domain）是一些轉錄因子中的高度保守的DNA結合結構域（DNA-binding domain，DBD）在超過40個物種（Pfam PF02362）中發現，與其它結構域一起（IPR003340）執行轉錄因子的功能。B3結構域的一級結構為100-120個胺基酸殘基，二級結構為七個β摺疊和兩個α螺旋，三級結構為假棒狀（pseudobarrel，Template:SCOP），從DNA結構的大溝處結合DNA分子[1]。

B3 蛋白家族

在擬南芥（Arabidopsis thaliana）中，有三個主要的轉錄因子家族帶有B3結構域[2]：

  • ARF（Auxin Response Factors）
  • ABI3（ABscisic acid Insensitive3）
  • RAV（Related to ABI3/VP1）
蛋白 ARF1-B3 ABI3-B3 RAV1-B3
B3 結構鑑定 分子建模[1] 分子建模[1] NMR[1]
B3 識別序列 TGTCTC[3][4] CATGCA[5][6] CACCTG[7]

PDB 1WID[1]和PDB 1YEL[8]是最早通過NMR解析過溶液狀態的B3結構域的結構

相關蛋白

限制性內切酶EcoRII的N端結構域，BfiI的C端結構域有和B3結構域類似的假棒狀三級結構[9][10]。

參考文獻

  1. ^ 1.0 1.1 1.2 1.3 1.4 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. 2004, 16 (12): 3448–59. PMC 535885 可免費查閱. PMID 15548737. doi:10.1105/tpc.104.026112. 
  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. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 2000, 290 (5499): 2105–10. Bibcode:2000Sci...290.2105R. PMID 11118137. doi:10.1126/science.290.5499.2105. 
  3. ^ Ulmasov T, Hagen G, Guilfoyle TJ. ARF1, a transcription factor that binds to auxin response elements. Science. 1997, 276 (5320): 1865–8. PMID 9188533. doi:10.1126/science.276.5320.1865. 
  4. ^ Tiwari SB, Hagen G, Guilfoyle TJ. The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription. Plant Cell. 2003, 15 (2): 533–43. PMC 141219 可免費查閱. PMID 12566590. doi:10.1105/tpc.008417. 
  5. ^ Suzuki M, Kao CY, McCarty DR. The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell. 1997, 9 (5): 799–807. PMC 156957 可免費查閱. PMID 9165754. doi:10.1105/tpc.9.5.799. 
  6. ^ 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. 2000, 24 (1): 57–66. PMID 11029704. doi:10.1046/j.1365-313x.2000.00857.x. 
  7. ^ 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. 1999, 27 (2): 470–8. PMC 148202 可免費查閱. PMID 9862967. doi:10.1093/nar/27.2.470. 
  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. 2005, 14 (9): 2478–83. PMC 2253459 可免費查閱. PMID 16081658. doi:10.1110/ps.051606305. 
  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. 2004, 335 (1): 307–19. PMID 14659759. doi: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 (PDF). Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (44): 15797–802 [2020-12-03]. Bibcode:2005PNAS..10215797G. PMC 1266039 可免費查閱. PMID 16247004. doi:10.1073/pnas.0507949102. （原始內容存檔 (PDF)於2017-09-22）. 
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