Affinage

Showing POLR2E — RPB5 is a alias.

POLR2E

DNA-directed RNA polymerases I, II, and III subunit RPABC1 · UniProt P19388

Length
210 aa
Mass
24.6 kDa
Annotated
2026-06-10
33 papers in source corpus 17 papers cited in narrative 17 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/6 claims corpus-supported (83%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLR2E (RPB5) is a structural subunit shared among all three eukaryotic nuclear RNA polymerases that integrates into the polymerase at the DNA cleft and also serves as a regulatory interface for transcription factors (PMID:9738888, PMID:10841537). Crystallographic analysis defined its bipartite architecture—a eukaryote-specific N-terminal domain and a C-terminal domain homologous to the archaeal RNAP subunit H—with distinct surface helices providing mapped binding sites (PMID:10841537). Within Pol II, RPB5 contacts Rpb1, Rpb2, and Rpb3, and its C-terminal globe engages the Rpb1 Bridge helix and Switch 1 loop regions to maintain the DNA-binding fold around the transcription bubble, cooperating with Rpb9 to hold this helix bundle in a packed conformation (PMID:9077438, PMID:17179178). The conserved central region of RPB5 is a direct binding platform: systematic alanine scanning shows that overlapping residues mediate interaction with the TFIIF subunit RAP30 and with the hepatitis B virus transactivator HBx, which compete for the same surface, while RPB5 also communicates with transcriptional activators and shares overlapping activation roles with the Rpb1 CTD (PMID:7828586, PMID:9860960, PMID:16169872). Beyond initiation, a specific rpb5 mutation impairs the Pol II transition into elongation by reducing Spt5 recruitment and increasing backtracking, and cryo-EM places RPB5 as a contact point for the elongation scaffold protein IWS1 [PMID:29133017, PMID:bio_10.1101_2025.08.28.672863]. RPB5 assembly and stability are governed by the unconventional prefoldin URI/RMP (yeast Bud27), which chaperones RPB5/RPB6 incorporation into the polymerases in the cytoplasm before nuclear import and, in the nucleus, modulates RPB5 stability and transcriptional output—repressing activated transcription by competing for TFIIB and TFIIF, repressing androgen-receptor-mediated transcription via Art-27, and competing with NRF2 for KEAP1 binding to control oxidative-stress responses (PMID:10712776, PMID:12737519, PMID:21730289, PMID:23459708, PMID:31541481).

Mechanistic history

Synthesis pass · year-by-year structured walk · 15 steps
  1. 1995 High

    Established that RPB5 is not merely a passive polymerase subunit but possesses a domain that communicates with transcriptional regulators, opening it as a regulatory target.

    Evidence In vitro deletion-mutant binding, co-IP from HepG2 cells, and CAT reporter assays mapping the HBx interaction to the central region

    PMID:7828586

    Open questions at the time
    • Did not resolve the structural basis of the central-region interaction
    • Physiological consequence for host transcription not defined
  2. 1996 Medium

    Defined where RPB5 sits within the polymerase by mapping its direct subunit contacts, establishing its topology in the Pol II complex.

    Evidence Far-Western blotting and in vitro binary complex formation in S. pombe

    PMID:9077438

    Open questions at the time
    • In vitro contacts not validated structurally at the time
    • Functional consequence of each contact untested
  3. 1998 High

    Showed that RPB5 contributes functionally to transcriptional activation and shares overlapping roles with the Rpb1 CTD, linking a structural subunit to activator response.

    Evidence rpb5-9 point-mutant in vitro transcription, in vivo reporters, synthetic lethality with CTD truncation, and human-yeast chimeric complementation

    PMID:9860960

    Open questions at the time
    • Molecular mechanism connecting RPB5 to activators not defined
    • Direct activator contact not identified
  4. 1998 Medium

    Demonstrated through region H interactions with both Rpb1 and the Pol I subunit Rpa190 that RPB5 is shared across the nuclear RNA polymerases.

    Evidence Yeast two-hybrid mapping with deletion fragments

    PMID:9738888

    Open questions at the time
    • Single interaction method
    • Pol III sharing not directly tested here
  5. 2000 High

    Resolved the bipartite architecture of RPB5 and localized regulator-binding surfaces, explaining how distinct partners engage discrete helices.

    Evidence X-ray crystallography of yeast RPB5 and NMR solution structure of the archaeal ortholog MtRPB5

    PMID:10841537 PMID:10841538

    Open questions at the time
    • Structure of human RPB5 not determined
    • Conformational changes upon partner binding not captured
  6. 2000 Medium

    Identified competition for TFIIB as the mechanism by which the RPB5 interactor RMP/URI antagonizes HBx-driven transactivation.

    Evidence In vitro competition pull-down for the d10 domain of TFIIB and CAT reporter rescue

    PMID:10712776

    Open questions at the time
    • Single-lab in vitro competition
    • In vivo relevance of TFIIB competition not established
  7. 2003 High

    Mapped the RMP/URI domain required to bind TFIIF and link this binding to repression of activated transcription.

    Evidence Far-Western, in vitro pull-down, co-IP from COS1 cells, and luciferase reporters with D5-deletion mutants

    PMID:12737519

    Open questions at the time
    • How TFIIF binding by RMP couples to RPB5 not resolved
    • Generality across promoters untested
  8. 2005 High

    Defined at residue resolution the overlapping RPB5 surface used by RAP30 and HBx, explaining their mutual competition.

    Evidence Two-step alanine-scanning mutagenesis with in vitro binding and mammalian-cell co-IP

    PMID:16169872

    Open questions at the time
    • Functional output of disrupting each residue in transcription not measured
    • Effect on assembled polymerase not tested
  9. 2004 Medium

    Explained the predominantly cytoplasmic localization of the RPB5 partner RMP/URI and identified DMAP1 as a factor driving its nuclear corepressor function.

    Evidence GFP-fusion imaging with CLS/NLS domain deletions, two-hybrid isolation of DMAP1, and corepressor reporter assays

    PMID:15367675

    Open questions at the time
    • No in vitro reconstitution of shuttling
    • Direct link between localization and RPB5 stability not shown
  10. 2013 High

    Identified URI/Bud27 as the chaperone that assembles RPB5 (and RPB6) into all three polymerases in the cytoplasm before nuclear import.

    Evidence Genetic rescue of bud27Δ by RPB5 overexpression, subcellular fractionation, and domain-deletion mapping in yeast

    PMID:23459708

    Open questions at the time
    • Direct biochemical reconstitution of assembly not shown
    • Human URI assembly role inferred by conservation
  11. 2011 High

    Connected nuclear URI-RPB5 binding to control of RPB5 protein stability and repression of androgen-receptor-driven transcription via Art-27.

    Evidence MS, co-IP, ChIP at the NKX-3.1 promoter, genome-wide profiling, and siRNA knockdown

    PMID:21730289

    Open questions at the time
    • Mechanism stabilizing RPB5 not molecularly defined
    • Phosphorylation signal upstream of URI unresolved
  12. 2013 Medium

    Linked URI nuclear/cytoplasmic shuttling to Pol II activity and CRM1-dependent export, coupling RPB5 stability to transcriptional state.

    Evidence Nuclear MS interactome, co-IP, and fractionation with α-amanitin, actinomycin-D, and leptomycin B

    PMID:23667685

    Open questions at the time
    • Single-lab pharmacological inference of CRM1 export
    • Direct RPB5 co-export not demonstrated
  13. 2017 High

    Assigned RPB5 a dedicated role in the Pol II-specific transition from initiation to productive elongation.

    Evidence rpb5-P151T mutant analysis with ChIP, run-on, Spt5 ChIP, CTD phosphorylation, and dst1Δ epistasis in yeast

    PMID:29133017

    Open questions at the time
    • Structural basis of how P151T alters backtracking not resolved
    • Whether the Spt5 recruitment defect is direct unclear
  14. 2020 High

    Extended the RMP/URI interactome to KEAP1, defining a competition-based mechanism that stabilizes NRF2 and drives antioxidant responses and tumorigenesis.

    Evidence Mouse ICC tumor model with RMP deletion, co-IP, ubiquitination and competition binding assays, and antioxidant gene profiling

    PMID:31541481

    Open questions at the time
    • Role of RPB5 itself versus free URI in this pathway not separated
    • Direct involvement of polymerase-bound RPB5 untested
  15. 2025 Medium

    Placed RPB5 within the active elongation complex as a direct contact point for the scaffold protein IWS1.

    Evidence Cryo-EM of the elongation complex with functional IWS1 SLiM mutants (preprint)

    PMID:bio_10.1101_2025.08.28.672863

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • Functional consequence of the RPB5-IWS1 contact for elongation not isolated

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RPB5's regulatory surface integrates competing partners (TFIIF, HBx, IWS1) with its structural role in maintaining the cleft during the initiation-to-elongation switch remains unresolved.
  • No structure of human RPB5 in an assembled, partner-bound polymerase
  • Quantitative ordering of competing partner exchange during the transcription cycle unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 4 GO:0140110 transcription regulator activity 2 GO:0003677 DNA binding 1
Localization
GO:0005634 nucleus 2 GO:0005829 cytosol 2
Pathway
R-HSA-74160 Gene expression (Transcription) 3 R-HSA-8953854 Metabolism of RNA 2
Partners
HBXIWS1RAP30RPB1RPB2RPB3TFIIBURI
Complex memberships
RNA polymerase IRNA polymerase IIRNA polymerase III

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 Human RPB5 (POLR2E) directly binds the HBx transactivation domain of hepatitis B virus X protein; the central region of human RPB5 is necessary for this interaction, demonstrated by in vitro deletion-mutant binding assays and co-immunoprecipitation from transfected HepG2 cells. The HBx-binding region of RPB5 alone stimulated transcription from reporters bearing X-responsive elements, indicating RPB5 has a domain that communicates with transcriptional regulators. In vitro binding assays with deletion mutants of fusion proteins; co-immunoprecipitation from transfected HepG2 cells; CAT reporter assay The EMBO journal High 7828586
1996 In fission yeast S. pombe, Rpb5 physically contacts Rpb1, Rpb2, and Rpb3 (and weakly Rpb5 itself and a 15-kDa subunit) within the RNA polymerase II complex, as shown by Far-Western blotting and in vitro binary complex formation, establishing the subunit-contact topology of RPB5 within the polymerase. Far-Western blot analysis using 32P-labeled GST-Rpb5 probe; in vitro complex formation with protein-immobilized beads Genes to cells : devoted to molecular & cellular mechanisms Medium 9077438
1998 A point mutation in RPB5 (rpb5-9) impairs transcriptional activation by GAL4-VP16 in vitro and in vivo, and is synthetically lethal with truncation of the RPB1 CTD, demonstrating that RPB5 and the CTD have overlapping roles in activation. The conserved central region of human RPB5 can functionally substitute for the corresponding yeast region, confirming functional conservation. In vitro transcription with mutant whole-cell extracts; reporter assays in vivo; Northern analysis; chimeric human-yeast RPB5 complementation; synthetic lethality analysis Proceedings of the National Academy of Sciences of the United States of America High 9860960
1998 Two-hybrid mapping in S. cerevisiae showed that Rpb5 interacts with region H of Rpb1 (conserved across all RNA polymerases, including bacterial β′), and that region H of RNA polymerase I subunit Rpa190 also interacts with Rpb5, consistent with RPB5 being shared among all three nuclear RNA polymerases. Yeast two-hybrid screening with deletion fragments of Rpb1 and Rpb2 Molecular & general genetics : MGG Medium 9738888
2000 Crystal structure of S. cerevisiae RPB5 revealed a bipartite architecture: a eukaryote-specific N-terminal domain and a C-terminal domain homologous to archaeal RNAP subunit H. The experimentally mapped interaction sites for TFIIB and HBx correspond to distinct, surface-exposed α-helical structures. X-ray crystallography Proceedings of the National Academy of Sciences of the United States of America High 10841537
2000 Solution NMR structure of the archaeal RPB5 ortholog (MtRPB5 from Methanobacterium thermoautotrophicum) revealed a four-stranded β-sheet platform with two flanking α-helices (mushroom shape), with conserved charged surface residues suggesting interaction interfaces with other proteins. NMR solution structure determination Proceedings of the National Academy of Sciences of the United States of America High 10841538
2000 RMP (URI/RPB5-mediating protein) and HBx compete for binding to the d10 domain of TFIIB (TF2B); RMP disrupts HBx–TFIIB interaction, and HBx disrupts RMP–TFIIB interaction in vitro, establishing competitive binding to TFIIB as the mechanism by which RMP represses HBx transactivation. In vitro pull-down (protein-protein binding competition assay); CAT reporter assay with TFIIB rescue Zhonghua gan zang bing za zhi Medium 10712776
2003 RMP (URI) binds both RAP30 and RAP74 subunits of TFIIF through its C-terminal D5 domain (118-aa residues), and this interaction is required for RMP to suppress activated transcription; deletion of D5 abolishes both TFIIF binding and transcriptional repression of Gal-VP16-activated reporters. In vitro pull-down; Far-Western analysis; co-immunoprecipitation from COS1 cells; luciferase reporter assay Cell research High 12737519
2004 RMP (URI) localizes predominantly to the cytoplasm via a coiled-coil cytoplasmic localization signal (CLS), with a nuclear localization signal (NLS) that is functional only in the absence of the CLS. DMAP1 binds the CC domain of RMP and facilitates its nuclear localization and corepressor activity in a dose-dependent manner. GFP-fusion live-cell imaging; yeast two-hybrid isolation of DMAP1; reporter assays for corepressor activity Molecular and cellular biology Medium 15367675
2005 Systematic alanine-scanning mutagenesis of the central region of human RPB5 identified residues critical for binding RAP30 (TFIIF) and/or HBx: F76, I104, T111, and S113 are critical for both interactions (overlapping binding site); V74 and N98 are required specifically for HBx binding; T56 and L58 are needed for RAP30 binding. Two-step alanine-scanning mutagenesis; in vitro binding assay; co-immunoprecipitation in mammalian cells Journal of biochemistry High 16169872
2006 Functional and structural analysis in S. cerevisiae showed that the C-terminal globe of Rpb5 contacts Rpb1-β25/26 (Bridge helix region) and Rpb1-α44/47 (Switch 1 loop region). These contacts are required to maintain the DNA-binding fold around the transcription bubble; rpb5 mutants affecting these contacts showed genetic synergy with rpb9Δ, suggesting Rpb5 and Rpb9 cooperate to hold the Bridge helix, Switch 1 loop, and Rpb1-α44/47 helix bundle in a packed conformation. Conditional/lethal mutant analysis; two-hybrid assay; genetic epistasis (synthetic lethality with rpb9Δ and rpa12Δ) Nucleic acids research Medium 17179178
2011 URI (unconventional prefoldin RPB5 interactor) binds RPB5/POLR2E in the nucleus, regulates RPB5 protein stability, and represses androgen receptor (AR)-mediated transcription. URI depletion increases AR occupancy at the NKX-3.1 promoter and decreases Art-27 (AR corepressor) recruitment; URI is phosphorylated upon androgen treatment. URI is present on chromatin prior to hormone-dependent AR recruitment. Mass spectrometry; co-immunoprecipitation; ChIP; genome-wide expression profiling; siRNA knockdown; reporter assays; phosphorylation detection Molecular and cellular biology High 21730289
2013 In yeast, Bud27 (ortholog of human URI) facilitates assembly of RPB5 and RPB6 into all three RNA polymerases in the cytoplasm prior to nuclear import; loss of BUD27 causes accumulation of RNA polymerases in the cytoplasm, a defect rescued by RPB5 overexpression. The Rpb5-binding domain (not the PFD-binding domain) of Bud27 is required for this assembly function. Genetic rescue (RPB5 overexpression suppressing bud27Δ phenotype); subcellular fractionation/localization; genetic interaction analysis; domain-deletion analysis PLoS genetics High 23459708
2013 URI binds RPB5/POLR2E in the nucleus, stabilizes RPB5 protein levels, and regulates transcription; URI nuclear/cytoplasmic shuttling is sensitive to compounds stalling Pol II (α-amanitin, actinomycin-D) and to leptomycin B (CRM1 inhibitor), suggesting CRM1-dependent nuclear export of URI together with Pol II subunits. URI also stabilizes PDRG1 protein through direct binding. Mass spectrometry-based proteomic analysis of nuclear URI interactors; co-immunoprecipitation; nuclear/cytoplasmic fractionation with drug treatments PloS one Medium 23667685
2017 The rpb5-P151T mutation in yeast specifically impairs RNA polymerase II transcription elongation (not Pol I or Pol III), causing increased backtracking shortly after initiation, reduced elongation rate, decreased Spt5 recruitment to chromatin, and altered Pol II CTD phosphorylation state. Genetic interaction with dst1Δ (TFIIS) confirmed the backtracking phenotype. ChIP; run-on analysis; genetic interactions (dst1Δ epistasis); CTD phosphorylation analysis; Spt5 ChIP Biochimica et biophysica acta. Gene regulatory mechanisms High 29133017
2020 RMP (URI/RPB5-mediating protein) competes with NRF2 for binding to the Kelch domain of KEAP1 via an E**E motif, leading to decreased ubiquitination-dependent NRF2 degradation, increased NRF2 nuclear translocation, and upregulation of antioxidant gene targets, thereby promoting cholangiocarcinoma tumorigenesis and drug resistance. Mouse ICC tumor model with RMP deletion; co-immunoprecipitation; ubiquitination assay; nuclear fractionation; competition binding assay; antioxidant gene expression analysis Hepatology High 31541481
2025 Cryo-EM mapping of the transcription elongation complex showed that IWS1 short linear motifs (SLiMs) directly contact RPB5 (POLR2E) as well as RPB1, RPB2, DSIF, SPT6, and ELOF1, positioning RPB5 as a structural contact point for the elongation scaffold protein IWS1 within the active elongation complex. Cryo-electron microscopy; functional assays for IWS1 SLiM mutants bioRxiv (preprint)preprint Medium bio_10.1101_2025.08.28.672863

Source papers

Stage 0 corpus · 33 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1995 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. The EMBO journal 230 7828586
2013 The prefoldin bud27 mediates the assembly of the eukaryotic RNA polymerases in an rpb5-dependent manner. PLoS genetics 62 23459708
2013 Analysis of URI nuclear interaction with RPB5 and components of the R2TP/prefoldin-like complex. PloS one 54 23667685
2015 Long noncoding RNAs POLR2E rs3787016 C/T and HULC rs7763881 A/C polymorphisms are associated with decreased risk of esophageal cancer. Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 52 25874495
1998 RNA polymerase subunit RPB5 plays a role in transcriptional activation. Proceedings of the National Academy of Sciences of the United States of America 45 9860960
2011 Regulation of androgen receptor-mediated transcription by RPB5 binding protein URI/RMP. Molecular and cellular biology 33 21730289
2011 RPB5-mediating protein is required for the proliferation of hepatocellular carcinoma cells. The Journal of biological chemistry 32 21310960
2000 Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proceedings of the National Academy of Sciences of the United States of America 32 10841537
2017 The HOTAIR, PRNCR1 and POLR2E polymorphisms are associated with cancer risk: a meta-analysis. Oncotarget 31 28159929
2003 Interaction with general transcription factor IIF (TFIIF) is required for the suppression of activated transcription by RPB5-mediating protein (RMP). Cell research 29 12737519
2006 Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic acids research 26 17179178
2004 Subcellular localization of RPB5-mediating protein and its putative functional partner. Molecular and cellular biology 25 15367675
1996 Molecular assembly of RNA polymerase II from the fission yeast Schizosaccharomyces pombe: subunit-subunit contact network involving Rpb5. Genes to cells : devoted to molecular & cellular mechanisms 25 9077438
2005 Mutational analysis of human RNA polymerase II subunit 5 (RPB5): the residues critical for interactions with TFIIF subunit RAP30 and hepatitis B virus X protein. Journal of biochemistry 20 16169872
2020 RPB5-Mediating Protein Promotes Cholangiocarcinoma Tumorigenesis and Drug Resistance by Competing With NRF2 for KEAP1 Binding. Hepatology (Baltimore, Md.) 19 31541481
2000 Solution structure of the RNA polymerase subunit RPB5 from Methanobacterium thermoautotrophicum. Proceedings of the National Academy of Sciences of the United States of America 17 10841538
1998 Mapping of Rpb3 and Rpb5 contact sites on two large subunits, Rpb1 and Rpb2, of the RNA polymerase II from fission yeast. Molecular & general genetics : MGG 16 9738888
2018 The association of POLR2E rs3787016 polymorphism and cancer risk: a Chinese case-control study and meta-analysis. Bioscience reports 8 30291213
1995 Sequence and functional analysis of a 7.2 kb DNA fragment containing four open reading frames located between RPB5 and CDC28 on the right arm of chromosome II. Yeast (Chichester, England) 8 7483850
2017 Rpb5 modulates the RNA polymerase II transition from initiation to elongation by influencing Spt5 association and backtracking. Biochimica et biophysica acta. Gene regulatory mechanisms 7 29133017
2015 RPB5-Mediating Protein Suppresses Hepatitis B Virus (HBV) Transcription and Replication by Counteracting the Transcriptional Activation of Hepatitis B virus X Protein in HBV Replication Mouse Model. Jundishapur journal of microbiology 7 26495109
2018 Long non-coding RNA POLR2E rs3787016 is associated with the risk of papillary thyroid carcinoma in Chinese population. Pathology, research and practice 6 29724531
2018 Long non-coding RNA POLR2E gene polymorphisms increased the risk of prostate cancer in a sample of the Iranian population. Nucleosides, nucleotides & nucleic acids 6 30587086
2000 [Study of HBV X protein and RMP, an RPB5 mediate protein competitively interacting with general transcription factor TF2B]. Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology 6 10712776
1999 Crystallization and preliminary diffraction studies of the RNA polymerase subunit RPB5 from Saccharomyces cerevisiae. Acta crystallographica. Section D, Biological crystallography 6 10393311
2018 Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI. AIMS genetics 5 31435513
2015 Cloning, soluble expression, and purification of the RNA polymerase II subunit RPB5 from Saccharomyces cerevisiae. Bioengineered 4 25551420
2014 Activation of a chimeric Rpb5/RpoH subunit using library selection. PloS one 4 24489922
2021 RPB5-mediating protein promotes the progression of non-small cell lung cancer by regulating the proliferation and invasion. Journal of thoracic disease 3 33569210
2024 Associations of long non-coding RNAs HOTAIR, LINC00951, POLR2E and HULC polymorphisms with the risk of esophageal and esophagogastric junction cancer in a western population: a case-control study. Molecular biology reports 2 38300349
2025 Evaluation of the role of unconventional prefoldin RPB5 interactor (URI1) in hepatitis B virus infection. Virology journal 1 39794779
2025 Protocatechuic Acid Alleviates Inflammation and Oxidative Stress in Acute Respiratory Distress Syndrome by Promoting Unconventional Prefoldin RPB5 Interactor 1-Mediated Mitophagy. Chemical biology & drug design 1 40040620
2011 Crystallization and preliminary X-ray analysis of the RPB5 subunit of human RNA polymerase II. Acta crystallographica. Section F, Structural biology and crystallization communications 1 22102239

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