Crystal Structure of RPB5, a Universal Eukaryotic RNA Polymerase Subunit and Transcription Factor Interaction Target

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2000 Jun 7

PMID 10841537

Citations 16

Authors

F Todone

R O Weinzierl

P Brick

S ONESTI

Affiliations

Soon will be listed here.

Abstract

Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.

Citing Articles

The Order-Disorder Continuum: Linking Predictions of Protein Structure and Disorder through Molecular Simulation.

Hsu C, Buehler M, Tarakanova A Sci Rep. 2020; 10(1):2068.

PMID: 32034199 PMC: 7005769. DOI: 10.1038/s41598-020-58868-w.

Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI.

Martinez-Fernandez V, Navarro F AIMS Genet. 2019; 5(1):63-74.

PMID: 31435513 PMC: 6690254. DOI: 10.3934/genet.2018.1.74.

Cloning, soluble expression, and purification of the RNA polymerase II subunit RPB5 from Saccharomyces cerevisiae.

Chhetri G, Ghosh A, Chinta R, Akhtar S, Tripathi T Bioengineered. 2015; 6(1):62-6.

PMID: 25551420 PMC: 4601343. DOI: 10.1080/21655979.2014.1002301.

Activation of a chimeric Rpb5/RpoH subunit using library selection.

Sommer B, Waege I, Pollmann D, Seitz T, Thomm M, Sterner R PLoS One. 2014; 9(1):e87485.

PMID: 24489922 PMC: 3906176. DOI: 10.1371/journal.pone.0087485.

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.

Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K Nucleic Acids Res. 2012; 40(15):7016-45.

PMID: 22638584 PMC: 3424549. DOI: 10.1093/nar/gks382.

References

Zaychikov E, Martin E, Denissova L, Kozlov M, Markovtsov V, Kashlev M . Mapping of catalytic residues in the RNA polymerase active center. Science. 1996; 273(5271):107-9. DOI: 10.1126/science.273.5271.107. View

Fu J, Gnatt A, Bushnell D, Jensen G, Thompson N, Burgess R . Yeast RNA polymerase II at 5 A resolution. Cell. 1999; 98(6):799-810. DOI: 10.1016/s0092-8674(00)81514-7. View

Thiru A, Hodach M, Eloranta J, Kostourou V, Weinzierl R, Matthews S . RNA polymerase subunit H features a beta-ribbon motif within a novel fold that is present in archaea and eukaryotes. J Mol Biol. 1999; 287(4):753-60. DOI: 10.1006/jmbi.1999.2638. View

Kolodziej P, Woychik N, Liao S, Young R . RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol. 1990; 10(5):1915-20. PMC: 360537. DOI: 10.1128/mcb.10.5.1915-1920.1990. View

Nicholls A, Sharp K, Honig B . Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991; 11(4):281-96. DOI: 10.1002/prot.340110407. View

DArcy T, HAUSNER W, Awery D, Edwards A, Thomm M, Reeve J . Methanobacterium thermoautotrophicum RNA polymerase and transcription in vitro. J Bacteriol. 1999; 181(14):4424-9. PMC: 93948. DOI: 10.1128/JB.181.14.4424-4429.1999. View

MIYAO T, Woychik N . RNA polymerase subunit RPB5 plays a role in transcriptional activation. Proc Natl Acad Sci U S A. 1998; 95(26):15281-6. PMC: 28034. DOI: 10.1073/pnas.95.26.15281. View

Jones T, Zou J, Cowan S, Kjeldgaard M . Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991; 47 ( Pt 2):110-9. DOI: 10.1107/s0108767390010224. View

Kabsch W, Sander C . Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983; 22(12):2577-637. DOI: 10.1002/bip.360221211. View

10.

Zhang G, Campbell E, Minakhin L, Richter C, Severinov K, Darst S . Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell. 1999; 98(6):811-24. DOI: 10.1016/s0092-8674(00)81515-9. View

11.

Esnouf R . An extensively modified version of MolScript that includes greatly enhanced coloring capabilities. J Mol Graph Model. 1997; 15(2):132-4, 112-3. DOI: 10.1016/S1093-3263(97)00021-1. View

12.

Young R . RNA polymerase II. Annu Rev Biochem. 1991; 60:689-715. DOI: 10.1146/annurev.bi.60.070191.003353. View

13.

Makino Y, Yogosawa S, Kayukawa K, Coin F, Egly J, Wang Z . TATA-Binding protein-interacting protein 120, TIP120, stimulates three classes of eukaryotic transcription via a unique mechanism. Mol Cell Biol. 1999; 19(12):7951-60. PMC: 84880. DOI: 10.1128/MCB.19.12.7951. View

14.

Cheong J, Yi M, Lin Y, Murakami S . Human RPB5, a subunit shared by eukaryotic nuclear RNA polymerases, binds human hepatitis B virus X protein and may play a role in X transactivation. EMBO J. 1995; 14(1):143-50. PMC: 398061. DOI: 10.1002/j.1460-2075.1995.tb06984.x. View

15.

Doolittle R, Feng D, Tsang S, Cho G, Little E . Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 1996; 271(5248):470-7. DOI: 10.1126/science.271.5248.470. View

16.

MIYAO T, Yasui K, Sakurai H, Yamagishi M, Ishihama A . Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit-subunit contact network involving Rpb5. Genes Cells. 1996; 1(9):843-54. DOI: 10.1046/j.1365-2443.1996.730274.x. View

17.

Hodach M, Todone F, Eloranta J, ONESTI S, Weinzierl R . Crystallization and preliminary diffraction studies of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae. Acta Crystallogr D Biol Crystallogr. 1999; 55(Pt 7):1373-5. DOI: 10.1107/s0907444999007271. View

18.

Gaskell A, Gilbert D, Ladias J, Wagner G . Solution structure of the hRPABC14.4 subunit of human RNA polymerases. Nat Struct Biol. 1999; 6(11):1039-42. DOI: 10.1038/14923. View

19.

Brunger A, Kuriyan J, Karplus M . Crystallographic R factor refinement by molecular dynamics. Science. 1987; 235(4787):458-60. DOI: 10.1126/science.235.4787.458. View

20.

Wang B, Jones D, Kaine B, Weiss M . High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases. Structure. 1998; 6(5):555-69. DOI: 10.1016/s0969-2126(98)00058-6. View