1y14

Structural highlights

Function

[RPB4_YEAST] 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. RPB4 is part of a subcomplex with RPB7 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex is necessary for promoter-directed transcription initiation but is not required for recruitment of Pol II to active preinitiation complexes and seems to be dispensable for transcription elongation and termination. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II. Involved in DNA repair of damage in the transcribed strand. RPB4 is dispensable under optimal growth conditions, but becomes essential during heat or cold shock and under nutrient depletion. Suppresses the RBP9-mediated transcription-coupled repair (TCR) subpathway of nucleotide excision repair (NER) but facilitates the RAD26-mediated TCR subpathway. Under stress conditions only, involved in mRNA export to the cytoplasm. Involved in mRNA decay. Promotes or enhances the deadenylation process of specific mRNAs and may recruit PAT1 and the LSM1-7 complex to these mRNAs, thus stimulating their decapping and further decay.^{[1] [2] [3] [4] [5] [6] [7]} [RPB7_YEAST] 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. RPB7 is part of a subcomplex with RPB4 that binds to a pocket formed by RPB1, RPB2 and RPB6 at the base of the clamp element. The RBP4-RPB7 subcomplex seems to lock the clamp via RPB7 in the closed conformation thus preventing double stranded DNA to enter the active site cleft. The RPB4-RPB7 subcomplex binds single-stranded DNA and RNA. The RPB4-RPB7 subcomplex recruits FCP1 to Pol II.^{[8] [9] [10]}

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

• RNA polymerase
• Temp1

References

1. ↑ Edwards AM, Kane CM, Young RA, Kornberg RD. Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J Biol Chem. 1991 Jan 5;266(1):71-5. PMID:1985924
2. ↑ Orlicky SM, Tran PT, Sayre MH, Edwards AM. Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem. 2001 Mar 30;276(13):10097-102. Epub 2000 Nov 21. PMID:11087726 doi:10.1074/jbc.M003165200
3. ↑ Pillai B, Sampath V, Sharma N, Sadhale P. Rpb4, a non-essential subunit of core RNA polymerase II of Saccharomyces cerevisiae is important for activated transcription of a subset of genes. J Biol Chem. 2001 Aug 17;276(33):30641-7. Epub 2001 May 29. PMID:11382749 doi:10.1074/jbc.M010952200
4. ↑ Li S, Smerdon MJ. Rpb4 and Rpb9 mediate subpathways of transcription-coupled DNA repair in Saccharomyces cerevisiae. EMBO J. 2002 Nov 1;21(21):5921-9. PMID:12411509
5. ↑ Farago M, Nahari T, Hammel C, Cole CN, Choder M. Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell. 2003 Jul;14(7):2744-55. PMID:12857861 doi:10.1091/mbc.E02-11-0740
6. ↑ Kamenski T, Heilmeier S, Meinhart A, Cramer P. Structure and mechanism of RNA polymerase II CTD phosphatases. Mol Cell. 2004 Aug 13;15(3):399-407. PMID:15304220 doi:http://dx.doi.org/10.1016/j.molcel.2004.06.035
7. ↑ Lotan R, Bar-On VG, Harel-Sharvit L, Duek L, Melamed D, Choder M. The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev. 2005 Dec 15;19(24):3004-16. PMID:16357218 doi:19/24/3004
8. ↑ Orlicky SM, Tran PT, Sayre MH, Edwards AM. Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem. 2001 Mar 30;276(13):10097-102. Epub 2000 Nov 21. PMID:11087726 doi:10.1074/jbc.M003165200
9. ↑ Kamenski T, Heilmeier S, Meinhart A, Cramer P. Structure and mechanism of RNA polymerase II CTD phosphatases. Mol Cell. 2004 Aug 13;15(3):399-407. PMID:15304220 doi:http://dx.doi.org/10.1016/j.molcel.2004.06.035
10. ↑ Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol. 2007 Sep 24;178(7):1133-43. Epub 2007 Sep 17. PMID:17875743 doi:10.1083/jcb.200701165
11. ↑ Armache KJ, Mitterweger S, Meinhart A, Cramer P. Structures of complete RNA polymerase II and its subcomplex, Rpb4/7. J Biol Chem. 2005 Feb 25;280(8):7131-4. Epub 2004 Dec 9. PMID:15591044 doi:10.1074/jbc.M413038200