| Structural highlights
6gml is a 21 chain structure with sequence from Human and Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| NonStd Res: | |
| Gene: | NELFA, WHSC2, P/OKcl.15 (HUMAN), NELFB, COBRA1, KIAA1182 (HUMAN), NELFCD, NELFD, TH1, TH1L, HSPC130 (HUMAN), NELFE, RD, RDBP (HUMAN), SUPT4H1, SPT4H, SUPT4H (HUMAN), SUPT5H, SPT5, SPT5H (HUMAN) |
| Activity: | DNA-directed RNA polymerase, with EC number 2.7.7.6 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Disease
[NELFA_HUMAN] Wolf-Hirschhorn syndrome.
Function
[RPB9_PIG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB9 is part of the upper jaw surrounding the central large cleft and thought to grab the incoming DNA template (By similarity). [NELFE_HUMAN] Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex.[1] [2] [3] [I3LGP4_PIG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.[RuleBase:RU363031] [SPT4H_HUMAN] component of the drb sensitivity-inducing factor complex (dsif complex), which regulates mrna processing and transcription elongation by rna polymerase ii dsif positively regulates mrna capping by stimulating the mrna guanylyltransferase activity of rngtt/cap1a dsif also acts cooperatively with the negative elongation factor complex (nelf complex) to enhance transcriptional pausing at sites proximal to the promoter transcriptional pausing may facilitate the assembly of an elongation competent rna polymerase ii complex dsif and nelf promote pausing by inhibition of the transcription elongation factor tfiis/s-ii tfiis/s-ii binds to rna polymerase ii at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme cleavage of blocked transcripts by rna polymerase ii promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites dsif can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the hiv- 1 nuclear transcriptional activator, tat dsif acts to suppress transcriptional pausing in transcripts derived from the hiv-1 ltr and blocks premature release of hiv-1 transcripts at terminator sequences [NELFD_HUMAN] Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex.[4] [5] [I3LCB2_PIG] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.[PIRNR:PIRNR000779] [NELFA_HUMAN] Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. Probably required to interact with the RNA polymerase II complex.[6] [7] [8] [NELFB_HUMAN] Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. Binds RNA which may help to stabilize the NELF complex on nucleic acid. In vitro, binds weakly to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1. May be able to induce chromatin unfolding.[9] [10] [11] [12] [SPT5H_HUMAN] Component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II. DSIF positively regulates mRNA capping by stimulating the mRNA guanylyltransferase activity of RNGTT/CAP1A. DSIF also acts cooperatively with the negative elongation factor complex (NELF complex) to enhance transcriptional pausing at sites proximal to the promoter. Transcriptional pausing may facilitate the assembly of an elongation competent RNA polymerase II complex. DSIF and NELF promote pausing by inhibition of the transcription elongation factor TFIIS/S-II. TFIIS/S-II binds to RNA polymerase II at transcription pause sites and stimulates the weak intrinsic nuclease activity of the enzyme. Cleavage of blocked transcripts by RNA polymerase II promotes the resumption of transcription from the new 3' terminus and may allow repeated attempts at transcription through natural pause sites. DSIF can also positively regulate transcriptional elongation and is required for the efficient activation of transcriptional elongation by the HIV-1 nuclear transcriptional activator, Tat. DSIF acts to suppress transcriptional pausing in transcripts derived from the HIV-1 LTR and blocks premature release of HIV-1 transcripts at terminator sequences.[13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31]
Publication Abstract from PubMed
Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we report the cryo-electron microscopy structure of a paused transcription elongation complex containing Sus scrofa Pol II and Homo sapiens DSIF and NELF at 3.2 A resolution. The structure reveals a tilted DNA-RNA hybrid that impairs binding of the nucleoside triphosphate substrate. NELF binds the polymerase funnel, bridges two mobile polymerase modules, and contacts the trigger loop, thereby restraining Pol II mobility that is required for pause release. NELF prevents binding of the anti-pausing transcription elongation factor IIS (TFIIS). Additionally, NELF possesses two flexible 'tentacles' that can contact DSIF and exiting RNA. These results define the paused state of Pol II and provide the molecular basis for understanding the function of NELF during promoter-proximal gene regulation.
Structure of paused transcription complex Pol II-DSIF-NELF.,Vos SM, Farnung L, Urlaub H, Cramer P Nature. 2018 Aug;560(7720):601-606. doi: 10.1038/s41586-018-0442-2. Epub 2018 Aug, 22. PMID:30135580[32]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
- ↑ Yamaguchi Y, Inukai N, Narita T, Wada T, Handa H. Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol Cell Biol. 2002 May;22(9):2918-27. PMID:11940650
- ↑ Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062
- ↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
- ↑ Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062
- ↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
- ↑ Zollino M, Lecce R, Fischetto R, Murdolo M, Faravelli F, Selicorni A, Butte C, Memo L, Capovilla G, Neri G. Mapping the Wolf-Hirschhorn syndrome phenotype outside the currently accepted WHS critical region and defining a new critical region, WHSCR-2. Am J Hum Genet. 2003 Mar;72(3):590-7. Epub 2003 Jan 30. PMID:12563561 doi:http://dx.doi.org/S0002-9297(07)60575-8
- ↑ Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062
- ↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
- ↑ Narita T, Yamaguchi Y, Yano K, Sugimoto S, Chanarat S, Wada T, Kim DK, Hasegawa J, Omori M, Inukai N, Endoh M, Yamada T, Handa H. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol Cell Biol. 2003 Mar;23(6):1863-73. PMID:12612062
- ↑ Natarajan M, Schiralli Lester GM, Lee C, Missra A, Wasserman GA, Steffen M, Gilmour DS, Henderson AJ. Negative elongation factor (NELF) coordinates RNA polymerase II pausing, premature termination, and chromatin remodeling to regulate HIV transcription. J Biol Chem. 2013 Sep 6;288(36):25995-6003. doi: 10.1074/jbc.M113.496489. Epub, 2013 Jul 24. PMID:23884411 doi:http://dx.doi.org/10.1074/jbc.M113.496489
- ↑ Vos SM, Pollmann D, Caizzi L, Hofmann KB, Rombaut P, Zimniak T, Herzog F, Cramer P. Architecture and RNA binding of the human negative elongation factor. Elife. 2016 Jun 10;5. pii: e14981. doi: 10.7554/eLife.14981. PMID:27282391 doi:http://dx.doi.org/10.7554/eLife.14981
- ↑ Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 1998 Feb 1;12(3):343-56. PMID:9450929
- ↑ Wu-Baer F, Lane WS, Gaynor RB. Role of the human homolog of the yeast transcription factor SPT5 in HIV-1 Tat-activation. J Mol Biol. 1998 Mar 27;277(2):179-97. PMID:9514752 doi:S0022-2836(97)91601-6
- ↑ Wada T, Takagi T, Yamaguchi Y, Watanabe D, Handa H. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. EMBO J. 1998 Dec 15;17(24):7395-403. PMID:9857195 doi:10.1093/emboj/17.24.7395
- ↑ Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H. NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell. 1999 Apr 2;97(1):41-51. PMID:10199401
- ↑ Parada CA, Roeder RG. A novel RNA polymerase II-containing complex potentiates Tat-enhanced HIV-1 transcription. EMBO J. 1999 Jul 1;18(13):3688-701. PMID:10393184 doi:10.1093/emboj/18.13.3688
- ↑ Wen Y, Shatkin AJ. Transcription elongation factor hSPT5 stimulates mRNA capping. Genes Dev. 1999 Jul 15;13(14):1774-9. PMID:10421630
- ↑ Yamaguchi Y, Wada T, Watanabe D, Takagi T, Hasegawa J, Handa H. Structure and function of the human transcription elongation factor DSIF. J Biol Chem. 1999 Mar 19;274(12):8085-92. PMID:10075709
- ↑ Kim JB, Yamaguchi Y, Wada T, Handa H, Sharp PA. Tat-SF1 protein associates with RAP30 and human SPT5 proteins. Mol Cell Biol. 1999 Sep;19(9):5960-8. PMID:10454543
- ↑ Wada T, Orphanides G, Hasegawa J, Kim DK, Shima D, Yamaguchi Y, Fukuda A, Hisatake K, Oh S, Reinberg D, Handa H. FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. Mol Cell. 2000 Jun;5(6):1067-72. PMID:10912001
- ↑ Ivanov D, Kwak YT, Guo J, Gaynor RB. Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol Cell Biol. 2000 May;20(9):2970-83. PMID:10757782
- ↑ Ping YH, Rana TM. DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 Tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J Biol Chem. 2001 Apr 20;276(16):12951-8. Epub 2000 Dec 8. PMID:11112772 doi:10.1074/jbc.M006130200
- ↑ Renner DB, Yamaguchi Y, Wada T, Handa H, Price DH. A highly purified RNA polymerase II elongation control system. J Biol Chem. 2001 Nov 9;276(45):42601-9. Epub 2001 Sep 11. PMID:11553615 doi:10.1074/jbc.M104967200
- ↑ Bourgeois CF, Kim YK, Churcher MJ, West MJ, Karn J. Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Mol Cell Biol. 2002 Feb;22(4):1079-93. PMID:11809800
- ↑ Kim DK, Inukai N, Yamada T, Furuya A, Sato H, Yamaguchi Y, Wada T, Handa H. Structure-function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex. Genes Cells. 2003 Apr;8(4):371-8. PMID:12653964
- ↑ Kwak YT, Guo J, Prajapati S, Park KJ, Surabhi RM, Miller B, Gehrig P, Gaynor RB. Methylation of SPT5 regulates its interaction with RNA polymerase II and transcriptional elongation properties. Mol Cell. 2003 Apr;11(4):1055-66. PMID:12718890
- ↑ Jennings BH, Shah S, Yamaguchi Y, Seki M, Phillips RG, Handa H, Ish-Horowicz D. Locus-specific requirements for Spt5 in transcriptional activation and repression in Drosophila. Curr Biol. 2004 Sep 21;14(18):1680-4. PMID:15380072 doi:10.1016/j.cub.2004.08.066
- ↑ Fujinaga K, Irwin D, Huang Y, Taube R, Kurosu T, Peterlin BM. Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol Cell Biol. 2004 Jan;24(2):787-95. PMID:14701750
- ↑ Mandal SS, Chu C, Wada T, Handa H, Shatkin AJ, Reinberg D. Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc Natl Acad Sci U S A. 2004 May 18;101(20):7572-7. Epub 2004 May 10. PMID:15136722 doi:10.1073/pnas.0401493101
- ↑ Palangat M, Renner DB, Price DH, Landick R. A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS. Proc Natl Acad Sci U S A. 2005 Oct 18;102(42):15036-41. Epub 2005 Oct 7. PMID:16214896 doi:10.1073/pnas.0409405102
- ↑ Vos SM, Farnung L, Urlaub H, Cramer P. Structure of paused transcription complex Pol II-DSIF-NELF. Nature. 2018 Aug;560(7720):601-606. doi: 10.1038/s41586-018-0442-2. Epub 2018 Aug, 22. PMID:30135580 doi:http://dx.doi.org/10.1038/s41586-018-0442-2
|
