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维基百科

DEAD box

四月 01, 2023

DEAD box為一蛋白質家族的通稱，在原核生物與真核生物細胞中皆有，因其中一個結構域有一天門冬胺酸-麩胺酸-丙胺酸-天門冬胺酸（DEAD）的氨基酸序列而得名[2]。此家族的蛋白多參與RNA相關反應[3]，有許多蛋白為RNA解旋酶[4]，可以消耗ATP的機制將雙股RNA解開[5]。

DEAD/DEAH box RNA解旋酶
釀酒酵母的eIF4A結構（1qva）[1]
鑑定
標誌DEAD
PfamPF00270（旧版）
Pfam宗系CL0023（旧版）
InterPro（英语：InterPro）IPR011545
PROSITE（英语：PROSITE）PDOC00039
SCOP（英语：Structural Classification of Proteins）1qva / SUPFAM
CDD（英语：Conserved Domain Database）cd00268
現有可用的蛋白結構：
Pfam結構（旧版） / ECOD
PDBRCSB PDB; PDBe; PDBj
PDBsum（英语：PDBsum）結構概要

DEAH家族與SKI2家族的蛋白序列也與DEAD box家族的蛋白相似[6][7][8]，三者合稱DExD/H家族蛋白[9]。

結構

1980年代晚期有學者發現許多蛋白的NTP結合位點（英语：NTP binding site）序列和eIF4ARNA解旋酶的相似[10]，後續研究發現這些蛋白均有9個保守的結構域，由N端至C端分別為Q結構域、結構域I、結構域Ia、結構域Ib、結構域II、結構域III、結構域IV、結構域V與結構域VI，其中結構域II又名沃克結構域-B（英语：Walker motifs），包含天門冬胺酸-麩胺酸-丙胺酸-天門冬胺酸（DEAD）的氨基酸序列[2]。Q結構域、結構域I、結構域II與結構域VI為結合與水解ATP所需，結構域Ia、結構域Ib、結構域III、結構域IV與結構域V則為結合RNA所需[11]。

功能

 
mRNA剪接過程，其中標註為橘色的蛋白皆屬DEAD box家族

DEAD box家族的蛋白多為RNA解旋酶，參與轉錄、RNA剪接、核糖體組裝（英语：ribosome biogenesis）、RNA轉運、轉譯與RNA降解等細胞中的多種RNA相關反應[9][12][13]。

釀酒酵母mRNA剪接的過程有Sub2、Prp28與Prp5等3種DEAD box蛋白參與[5]，其中Prp5可與U2 SnRNA（英语：U2 spliceosomal RNA）結合以影響其結構，使其得以與mRNA內含子中的分支位點（branchpoint）結合[14]；Prp28可能可識別內含子的5′端切割位點，但此蛋白無解旋酶活性[15]。另外Prp2、Prp16、Prp22、Prp43與Brr213等多種DEAH家族蛋白也參與mRNA剪切[16]。

轉譯起始因子eIF4A為一DEAD box蛋白，在轉譯起始時可解開mRNA5′ UTR的二級結構，以利核糖體小次單元掃描mRNA以尋找起始密碼子[17]。另一DEAD box Ded1也參與轉譯起始過程，但具體機制仍不明[18]；還有一與Ded1相似的DEAD box蛋白Vasa可與eIF2互動[19]。

參考文獻

  1. ^ Johnson, E. R.; McKay, D. B. Crystallographic structure of the amino terminal domain of yeast initiation factor 4A, a representative DEAD-box RNA helicase. RNA. 1999, 5 (12): 1526–1534. PMC 1369875  . PMID 10606264. doi:10.1017/S1355838299991410. 
  2. ^ 2.0 2.1 Linder, P.; Lasko, P. F.; Ashburner, M.; Leroy, P.; Nielsen, P. J.; Nishi, K.; Schnier, J.; Slonimski, P. P. Birth of the D-E-A-D box. Nature. 1989, 337 (6203): 121–122. Bibcode:1989Natur.337..121L. PMID 2563148. S2CID 13529955. doi:10.1038/337121a0. 
  3. ^ Takashi Kikuma; Masaya Ohtsu; Takahiko Utsugi; Shoko Koga; Kohji Okuhara; Toshihiko Eki; Fumihiro Fujimori; Yasufumi Murakami. Dbp9p, a Member of the DEAD Box Protein Family, Exhibits DNA Helicase Activity. J. Biol. Chem. March 2004, 279 (20): 20692–20698. PMID 15028736. doi:10.1074/jbc.M400231200  . 
  4. ^ Heung LJ, Del Poeta M. Unlocking the DEAD-box: a key to cryptococcal virulence?. J. Clin. Invest. March 2005, 115 (3): 593–5. PMC 1052016  . PMID 15765144. doi:10.1172/JCI24508. 
  5. ^ 5.0 5.1 Linder P. Dead-box proteins: a family affair—active and passive players in RNP-remodeling. Nucleic Acids Res. 2006, 34 (15): 4168–80. PMC 1616962  . PMID 16936318. doi:10.1093/nar/gkl468. 
  6. ^ Tanaka N, Schwer B. Characterization of the NTPase, RNA-binding, and RNA helicase activities of the DEAH-box splicing factor Prp22. Biochemistry. July 2005, 44 (28): 9795–803. PMID 16008364. doi:10.1021/bi050407m. 
  7. ^ Xu J, Wu H, Zhang C, Cao Y, Wang L, Zeng L, Ye X, Wu Q, Dai J, Xie Y, Mao Y. Identification of a novel human DDX40gene, a new member of the DEAH-box protein family. J. Hum. Genet. 2002, 47 (12): 681–3. PMID 12522690. doi:10.1007/s100380200104  . 
  8. ^ Wang L, Lewis MS, Johnson AW. Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p. RNA. August 2005, 11 (8): 1291–302. PMC 1370812  . PMID 16043509. doi:10.1261/rna.2060405. 
  9. ^ 9.0 9.1 de la Cruz J, Kressler D, Linder P. Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem. Sci. May 1999, 24 (5): 192–8. PMID 10322435. doi:10.1016/S0968-0004(99)01376-6. 
  10. ^ Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. June 1989, 17 (12): 4713–30. PMC 318027  . PMID 2546125. doi:10.1093/nar/17.12.4713. 
  11. ^ Tanner NK, Cordin O, Banroques J, Doère M, Linder P. The Q motif: a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis. Mol. Cell. January 2003, 11 (1): 127–38. PMID 12535527. doi:10.1016/S1097-2765(03)00006-6  . 
  12. ^ Aubourg S, Kreis M, Lecharny A. The DEAD box RNA helicase family in Arabidopsis thaliana. Nucleic Acids Res. January 1999, 27 (2): 628–36. PMC 148225  . PMID 9862990. doi:10.1093/nar/27.2.628. 
  13. ^ Staley JP, Guthrie C. Mechanical devices of the spliceosome: motors, clocks, springs, and things. Cell. February 1998, 92 (3): 315–26. PMID 9476892. S2CID 6208113. doi:10.1016/S0092-8674(00)80925-3  . 
  14. ^ Ghetti A, Company M, Abelson J. Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs. RNA. April 1995, 1 (2): 132–45. PMC 1369067  . PMID 7585243. 
  15. ^ Strauss EJ, Guthrie C. PRP28, a 'DEAD-box' protein, is required for the first step of mRNA splicing in vitro. Nucleic Acids Res. August 1994, 22 (15): 3187–93. PMC 310295  . PMID 7520570. doi:10.1093/nar/22.15.3187. 
  16. ^ Silverman E, Edwalds-Gilbert G, Lin RJ. DExD/H-box proteins and their partners: helping RNA helicases unwind. Gene. July 2003, 312: 1–16. PMID 12909336. doi:10.1016/S0378-1119(03)00626-7. 
  17. ^ Sonenberg N. Cap-binding proteins of eukaryotic messenger RNA: functions in initiation and control of translation. Prog. Nucleic Acid Res. Mol. Biol. Progress in Nucleic Acid Research and Molecular Biology. 1988, 35: 173–207. ISBN 978-0-12-540035-0. PMID 3065823. doi:10.1016/S0079-6603(08)60614-5. 
  18. ^ Berthelot K, Muldoon M, Rajkowitsch L, Hughes J, McCarthy JE. Dynamics and processivity of 40S ribosome scanning on mRNA in yeast. Mol. Microbiol. February 2004, 51 (4): 987–1001. PMID 14763975. doi:10.1046/j.1365-2958.2003.03898.x  . 
  19. ^ Carrera P, Johnstone O, Nakamura A, Casanova J, Jäckle H, Lasko P. VASA mediates translation through interaction with a Drosophila yIF2 homolog. Mol. Cell. January 2000, 5 (1): 181–7. PMID 10678180. doi:10.1016/S1097-2765(00)80414-1. hdl:11858/00-001M-0000-0012-F80E-6  . 

四月 01, 2023
dead, 為一蛋白質家族的通稱, 在原核生物與真核生物細胞中皆有, 因其中一個結構域有一天門冬胺酸, 麩胺酸, 丙胺酸, 天門冬胺酸, dead, 的氨基酸序列而得名, 此家族的蛋白多參與rna相關反應, 有許多蛋白為rna解旋酶, 可以消耗atp的機制將雙股rna解開, dead, deah, rna解旋酶釀酒酵母的eif4a結構, 1qva, 鑑定標誌deadpfampf00270, 旧版, pfam宗系cl0023, 旧版, interpro, 英语, interpro, ipr011545prosite,. DEAD box為一蛋白質家族的通稱 在原核生物與真核生物細胞中皆有 因其中一個結構域有一天門冬胺酸 麩胺酸 丙胺酸 天門冬胺酸 DEAD 的氨基酸序列而得名 2 此家族的蛋白多參與RNA相關反應 3 有許多蛋白為RNA解旋酶 4 可以消耗ATP的機制將雙股RNA解開 5 DEAD DEAH box RNA解旋酶釀酒酵母的eIF4A結構 1qva 1 鑑定標誌DEADPfamPF00270 旧版 Pfam宗系CL0023 旧版 InterPro 英语 InterPro IPR011545PROSITE 英语 PROSITE PDOC00039SCOP 英语 Structural Classification of Proteins 1qva SUPFAMCDD 英语 Conserved Domain Database cd00268現有可用的蛋白結構 Pfam結構 旧版 ECODPDBRCSB PDB PDBe PDBjPDBsum 英语 PDBsum 結構概要DEAH家族與SKI2家族的蛋白序列也與DEAD box家族的蛋白相似 6 7 8 三者合稱DExD H家族蛋白 9 結構 编辑1980年代晚期有學者發現許多蛋白的NTP結合位點 英语 NTP binding site 序列和eIF4ARNA解旋酶的相似 10 後續研究發現這些蛋白均有9個保守的結構域 由N端至C端分別為Q結構域 結構域I 結構域Ia 結構域Ib 結構域II 結構域III 結構域IV 結構域V與結構域VI 其中結構域II又名沃克結構域 B 英语 Walker motifs 包含天門冬胺酸 麩胺酸 丙胺酸 天門冬胺酸 DEAD 的氨基酸序列 2 Q結構域 結構域I 結構域II與結構域VI為結合與水解ATP所需 結構域Ia 結構域Ib 結構域III 結構域IV與結構域V則為結合RNA所需 11 功能 编辑 mRNA剪接過程 其中標註為橘色的蛋白皆屬DEAD box家族 DEAD box家族的蛋白多為RNA解旋酶 參與轉錄 RNA剪接 核糖體組裝 英语 ribosome biogenesis RNA轉運 轉譯與RNA降解等細胞中的多種RNA相關反應 9 12 13 釀酒酵母mRNA剪接的過程有Sub2 Prp28與Prp5等3種DEAD box蛋白參與 5 其中Prp5可與U2 SnRNA 英语 U2 spliceosomal RNA 結合以影響其結構 使其得以與mRNA內含子中的分支位點 branchpoint 結合 14 Prp28可能可識別內含子的5 端切割位點 但此蛋白無解旋酶活性 15 另外Prp2 Prp16 Prp22 Prp43與Brr213等多種DEAH家族蛋白也參與mRNA剪切 16 轉譯起始因子eIF4A為一DEAD box蛋白 在轉譯起始時可解開mRNA5 UTR的二級結構 以利核糖體小次單元掃描mRNA以尋找起始密碼子 17 另一DEAD box Ded1也參與轉譯起始過程 但具體機制仍不明 18 還有一與Ded1相似的DEAD box蛋白Vasa可與eIF2互動 19 參考文獻 编辑 分子与细胞生物学主题 Johnson E R McKay D B Crystallographic structure of the amino terminal domain of yeast initiation factor 4A a representative DEAD box RNA helicase RNA 1999 5 12 1526 1534 PMC 1369875 PMID 10606264 doi 10 1017 S1355838299991410 2 0 2 1 Linder P Lasko P F Ashburner M Leroy P Nielsen P J Nishi K Schnier J Slonimski P P Birth of the D E A D box Nature 1989 337 6203 121 122 Bibcode 1989Natur 337 121L PMID 2563148 S2CID 13529955 doi 10 1038 337121a0 Takashi Kikuma Masaya Ohtsu Takahiko Utsugi Shoko Koga Kohji Okuhara Toshihiko Eki Fumihiro Fujimori Yasufumi Murakami Dbp9p a Member of the DEAD Box Protein Family Exhibits DNA Helicase Activity J Biol Chem March 2004 279 20 20692 20698 PMID 15028736 doi 10 1074 jbc M400231200 Heung LJ Del Poeta M Unlocking the DEAD box a key to cryptococcal virulence J Clin Invest March 2005 115 3 593 5 PMC 1052016 PMID 15765144 doi 10 1172 JCI24508 5 0 5 1 Linder P Dead box proteins a family affair active and passive players in RNP remodeling Nucleic Acids Res 2006 34 15 4168 80 PMC 1616962 PMID 16936318 doi 10 1093 nar gkl468 Tanaka N Schwer B Characterization of the NTPase RNA binding and RNA helicase activities of the DEAH box splicing factor Prp22 Biochemistry July 2005 44 28 9795 803 PMID 16008364 doi 10 1021 bi050407m Xu J Wu H Zhang C Cao Y Wang L Zeng L Ye X Wu Q Dai J Xie Y Mao Y Identification of a novel human DDX40gene a new member of the DEAH box protein family J Hum Genet 2002 47 12 681 3 PMID 12522690 doi 10 1007 s100380200104 Wang L Lewis MS Johnson AW Domain interactions within the Ski2 3 8 complex and between the Ski complex and Ski7p RNA August 2005 11 8 1291 302 PMC 1370812 PMID 16043509 doi 10 1261 rna 2060405 9 0 9 1 de la Cruz J Kressler D Linder P Unwinding RNA in Saccharomyces cerevisiae DEAD box proteins and related families Trends Biochem Sci May 1999 24 5 192 8 PMID 10322435 doi 10 1016 S0968 0004 99 01376 6 Gorbalenya AE Koonin EV Donchenko AP Blinov VM Two related superfamilies of putative helicases involved in replication recombination repair and expression of DNA and RNA genomes Nucleic Acids Res June 1989 17 12 4713 30 PMC 318027 PMID 2546125 doi 10 1093 nar 17 12 4713 Tanner NK Cordin O Banroques J Doere M Linder P The Q motif a newly identified motif in DEAD box helicases may regulate ATP binding and hydrolysis Mol Cell January 2003 11 1 127 38 PMID 12535527 doi 10 1016 S1097 2765 03 00006 6 Aubourg S Kreis M Lecharny A The DEAD box RNA helicase family in Arabidopsis thaliana Nucleic Acids Res January 1999 27 2 628 36 PMC 148225 PMID 9862990 doi 10 1093 nar 27 2 628 Staley JP Guthrie C Mechanical devices of the spliceosome motors clocks springs and things Cell February 1998 92 3 315 26 PMID 9476892 S2CID 6208113 doi 10 1016 S0092 8674 00 80925 3 Ghetti A Company M Abelson J Specificity of Prp24 binding to RNA a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs RNA April 1995 1 2 132 45 PMC 1369067 PMID 7585243 Strauss EJ Guthrie C PRP28 a DEAD box protein is required for the first step of mRNA splicing in vitro Nucleic Acids Res August 1994 22 15 3187 93 PMC 310295 PMID 7520570 doi 10 1093 nar 22 15 3187 Silverman E Edwalds Gilbert G Lin RJ DExD H box proteins and their partners helping RNA helicases unwind Gene July 2003 312 1 16 PMID 12909336 doi 10 1016 S0378 1119 03 00626 7 Sonenberg N Cap binding proteins of eukaryotic messenger RNA functions in initiation and control of translation Prog Nucleic Acid Res Mol Biol Progress in Nucleic Acid Research and Molecular Biology 1988 35 173 207 ISBN 978 0 12 540035 0 PMID 3065823 doi 10 1016 S0079 6603 08 60614 5 Berthelot K Muldoon M Rajkowitsch L Hughes J McCarthy JE Dynamics and processivity of 40S ribosome scanning on mRNA in yeast Mol Microbiol February 2004 51 4 987 1001 PMID 14763975 doi 10 1046 j 1365 2958 2003 03898 x Carrera P Johnstone O Nakamura A Casanova J Jackle H Lasko P VASA mediates translation through interaction with a Drosophila yIF2 homolog Mol Cell January 2000 5 1 181 7 PMID 10678180 doi 10 1016 S1097 2765 00 80414 1 hdl 11858 00 001M 0000 0012 F80E 6 取自 https zh wikipedia org w index php title DEAD box amp oldid 74140248, 维基百科，wiki，书籍，书籍，图书馆，

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