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B3结构域

维基百科，自由的百科全书
B3 DNA binding domain
RAV1的B3 DNA结合结构域
鉴定
标志B3_domain
PfamPF02362（旧版）
InterPro（英语：InterPro）IPR003340
PROSITE（英语：PROSITE）PS50863
SCOP（英语：Structural Classification of Proteins）1wid / SUPFAM
CDD（英语：Conserved Domain Database）cd10017

B3 DNA结合结构域（英语：B3 DNA binding domain）是一些转录因子中的高度保守的DNA结合结构域（DNA-binding domain，DBD）在超过40个物种（Pfam PF02362）中发现，与其它结构域一起（IPR003340）执行转录因子的功能。B3结构域的一级结构为100-120个氨基酸残基，二级结构为七个β折叠和两个α螺旋，三级结构为假棒状（pseudobarrel，Template:SCOP），从DNA结构的大沟处结合DNA分子[1]。

B3 蛋白家族

在拟南芥（Arabidopsis thaliana）中，有三个主要的转录因子家族带有B3结构域[2]：

  • ARF（Auxin Response Factors）
  • ABI3（ABscisic acid Insensitive3）
  • RAV（Related to ABI3/VP1）
蛋白 ARF1-B3 ABI3-B3 RAV1-B3
B3 结构鉴定 分子建模[1] 分子建模[1] NMR[1]
B3 识别序列 TGTCTC[3][4] CATGCA[5][6] CACCTG[7]

PDB 1WID[1]和PDB 1YEL[8]是最早通过NMR解析过溶液状态的B3结构域的结构

相关蛋白

限制性内切酶EcoRII的N端结构域，BfiI的C端结构域有和B3结构域类似的假棒状三级结构[9][10]。

参考文献

  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 可免费查阅. 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 可免费查阅. 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 可免费查阅. 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 可免费查阅. 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 可免费查阅. 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 可免费查阅. PMID 16247004. doi:10.1073/pnas.0507949102. （原始内容存档 (PDF)于2017-09-22）. 
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