Affinage

POLR3K

DNA-directed RNA polymerase III subunit RPC10 · UniProt Q9Y2Y1

Length
108 aa
Mass
12.3 kDa
Annotated
2026-06-10
29 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POLR3K (RPC11/hRPC11) is the smallest RNA polymerase III-specific subunit and functions as a bifunctional zinc-ribbon protein that couples Pol III catalytic proofreading to transcription termination and tRNA processing (PMID:15632064, PMID:21450810). Its C-terminal TFIIS-homologous zinc ribbon catalyzes intrinsic RNA 3'-5' cleavage within the Pol III active site, controlling the length of 3'-oligo(U) tracts on nascent pre-tRNAs; because oligo(U) length governs La protein binding, this cleavage activity directs pre-tRNAs toward a La-independent maturation pathway (PMID:15632064). Its N-terminal Rpb9-homologous domain is functionally separable, mediating Pol III transcription termination through a hydrophobic patch (Y30, F32, I34) that interfaces with subunit C53/37 at the enzyme's upper jaw, integrating action between the upper jaw and the catalytic center (PMID:21450810). POLR3K is incorporated into the Pol III complex through direct interaction with POLR3B, and this functional partnership is conserved across vertebrates and yeast (PMID:18044988). Pol III output is further tuned by POLR3K cooperation with Rpc53 phosphorylation downstream of TORC1, repressing tRNA synthesis under nutrient limitation (PMID:22364741). Disease-causing POLR3K missense mutations partition along this domain architecture: R41W selectively impairs RNA 3' cleavage while sparing termination, and D108Y and the POLR3K-disrupting interface mutations reduce assembly and Pol III output, producing selective deficits in tRNA and other Pol III transcripts that underlie hypomyelinating leukodystrophy (PMID:30584594, PMID:40651364, PMID:40225923).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1998 Low

    Establishing the domain architecture of the human protein was the first step toward predicting its role in Pol III, identifying an N-terminal Zn-binding motif and a C-terminal TFIIS-homologous zinc ribbon.

    Evidence RT-PCR cloning and cDNA/domain homology analysis of human hRPC11

    PMID:10079944

    Open questions at the time
    • Sequence/domain prediction only with no functional experiment
    • No demonstration that either domain is catalytically or functionally active
    • No assignment of the domains to specific Pol III activities
  2. 2005 High

    It was unknown how Pol III limits 3'-oligo(U) tract length on pre-tRNAs; mutagenesis showed the Rpc11p zinc ribbon catalyzes RNA 3' cleavage and thereby sets oligo(U) length and downstream La-dependent versus La-independent processing.

    Evidence Zinc-ribbon site-directed mutagenesis with in vivo tRNA suppressor assay and 3'-oligo(U) RNA analysis in S. pombe

    PMID:15632064

    Open questions at the time
    • Did not separate cleavage from termination function
    • Catalytic mechanism inferred genetically rather than from reconstituted enzyme
    • Conservation to vertebrate POLR3K not yet tested
  3. 2007 High

    Whether POLR3B-POLR3K interactions and the cleavage/recycling role were conserved in vertebrates was open; rescue of a polr3b mutant by polr3k cDNA showed the phenotype reflects Rpc11 deficiency and a conserved POLR3B-POLR3K partnership.

    Evidence Genetic rescue in zebrafish slim jim (polr3b) mutants plus S. pombe Pol III subunit composition analysis

    PMID:18044988

    Open questions at the time
    • Did not map which POLR3K domain mediates POLR3B binding
    • Mechanism of polymerase recycling not directly resolved
    • Tissue-specific requirements not addressed
  4. 2011 High

    It was unclear whether termination and cleavage are one activity or two; domain-specific mutagenesis separated them, assigning termination to the N-terminal Rpb9-homologous domain (via a hydrophobic patch contacting C53/37) and cleavage to the C-terminal TFIIS-homologous domain.

    Evidence Random and site-directed mutagenesis with in vivo terminator readthrough assays and cryo-EM-guided structural modeling in S. pombe

    PMID:21450810

    Open questions at the time
    • C53/37 interface inferred from modeling, not co-structure
    • Coupling between upper-jaw and active-center actions during termination not directly visualized
    • Human POLR3K residues not functionally tested
  5. 2011 Medium

    A synthesis consolidated the link between Rpc11 cleavage activity, 3'-oligo(U) length, and La-dependent tRNA processing-pathway selection.

    Evidence Review integrating genetic and biochemical S. pombe rpc11 and tRNA-processing studies

    PMID:21572561

    Open questions at the time
    • No new primary data
    • Does not extend findings beyond yeast
    • Quantitative determinants of pathway choice not defined
  6. 2012 Medium

    How Pol III activity is downregulated under nutrient stress was unresolved; Rpc11 was shown to cooperate with TORC1-driven Rpc53 phosphorylation by Kns1/Mck1 to inhibit tRNA synthesis.

    Evidence Genetic epistasis, rapamycin treatment, kinase-mutant and phosphorylation analysis in S. cerevisiae

    PMID:22364741

    Open questions at the time
    • Molecular nature of Rpc11-Rpc53 cooperation not defined
    • Whether this regulation operates in vertebrate POLR3K untested
    • Direct effect on cleavage vs termination not separated
  7. 2018 Medium

    The first POLR3K disease mechanism was defined: the R41W variant disrupts POLR3K-POLR3B interaction and reduces Pol III RNA output, linking subunit assembly defects to pathology.

    Evidence Homozygosity mapping/exome sequencing in patients, structural analysis, zebrafish gut assay, RNA analysis of patient fibroblasts (5S, 7SL)

    PMID:30584594

    Open questions at the time
    • Interaction disruption based on structural modeling
    • Did not separate assembly defect from cleavage/termination defect
    • Mechanistic basis of leukodystrophy not directly addressed
  8. 2024 Medium

    Additional pathogenic variants refined genotype-function relationships, showing D108Y (steric interference) and a last-exon deletion (amorphic truncation) reduce POLR3K levels and selectively lower specific tRNA species while sparing other Pol III transcripts, indicating partial Pol III function.

    Evidence NGS, patient-cell RNA expression analysis, structural prediction, and tRNA quantification

    PMID:40225923

    Open questions at the time
    • Structural effect of D108Y predicted, not measured
    • Basis for tRNA-species selectivity unexplained
    • Link to myelination not directly tested
  9. 2025 High

    Whether the R41W leukodystrophy mutation acts through cleavage or termination was directly tested; yeast modeling showed it specifically impairs RNA 3' cleavage while sparing termination, lengthens tRNA 3'-oligo(U), and is lethal with sen1 deletion.

    Evidence Site-directed mutagenesis in S. cerevisiae and S. pombe with in vitro cleavage and termination assays, growth assays, oligo(U) analysis, and sen1 epistasis

    PMID:40651364

    Open questions at the time
    • Direct demonstration in human cells not performed
    • How impaired cleavage produces hypomyelination not resolved
    • Reconciliation with the R41W assembly defect reported earlier not addressed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How POLR3K cleavage/termination defects and reduced tRNA/rRNA output mechanistically cause hypomyelinating leukodystrophy remains unresolved.
  • No mechanism linking tRNA-pool changes to myelination
  • No human-cell or co-structure validation of variant effects on Pol III activity
  • Cell-type specificity of disease unexplained

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0005198 structural molecule activity 2 GO:0140098 catalytic activity, acting on RNA 2
Localization
GO:0005634 nucleus 2
Pathway
R-HSA-74160 Gene expression (Transcription) 3 R-HSA-8953854 Metabolism of RNA 2
Partners
C53/37POLR3BRPC53
Complex memberships
RNA polymerase III

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 POLR3K (Rpc11/polr3k) is required for RNA cleavage activity and recycling of RNA polymerase III; the zebrafish slim jim mutation in polr3b causes deficiency of the Rpc11 subunit, and overexpression of polr3k cDNA rescues the exocrine defects in slim jim mutants, demonstrating that the phenotype is due to Rpc11 deficiency and that POLR3B–POLR3K functional interactions are conserved in vertebrates. Genetic rescue (overexpression of polr3k cDNA in zebrafish slim jim mutants), engineered S. pombe rpc2-delta mutation with Pol III subunit composition analysis PLoS biology High 18044988
2005 The zinc ribbon domain of Rpc11p (POLR3K ortholog) mediates RNA 3'-5' cleavage activity within the Pol III catalytic center; zinc ribbon mutants deficient in RNA 3' cleavage produce pre-tRNAs with elongated 3'-oligo(U) tracts that become better substrates for La protein, demonstrating that Rpc11p limits 3'-U length and thereby directs pre-tRNAs toward a La-independent maturation pathway. In vivo tRNA suppressor assay in S. pombe, site-directed mutagenesis of zinc ribbon motifs, RNA analysis of 3'-oligo(U) tract length Molecular and cellular biology High 15632064
2011 Mutations in the Rpb9-homologous (N-terminal) domain of Rpc11p (e.g., Y30, F32, I34) impair transcription termination by Pol III without abolishing RNA 3' cleavage, whereas mutations in the TFIIS-homologous (C-terminal) domain affect RNA 3' cleavage; residues F32, I34, Y30 are predicted to form a hydrophobic patch that interfaces with subunit C53/37, integrating action at the upper jaw and catalytic center during termination. In vivo terminator readthrough assay in S. pombe, random and site-directed mutagenesis, RNA analysis of terminator readthrough transcripts, structural modeling with cryo-EM data Nucleic acids research High 21450810
2011 Pol III-intrinsic 3' exonuclease activity mediated by Rpc11p (POLR3K ortholog) affects the length of 3'-oligo(U) tracts on precursor tRNAs, which is a primary determinant of La protein binding and subsequent tRNA processing pathway selection. Review synthesizing genetic and biochemical data from multiple S. pombe studies using rpc11 mutants and tRNA processing assays Wiley interdisciplinary reviews. RNA Medium 21572561
2012 Rpc11 (POLR3K ortholog) cooperates with phosphorylation of Pol III subunit Rpc53 (mediated by LAMMER kinase Kns1 and GSK-3 kinase Mck1 downstream of TORC1) to modify Pol III enzyme function and inhibit tRNA synthesis in response to nutrient limitation and rapamycin treatment. Genetic epistasis in S. cerevisiae, rapamycin treatment, kinase mutant analysis, phosphorylation assays Molecular cell Medium 22364741
2018 A disease-causing missense mutation in POLR3K (c.121C>T/p.Arg41Trp) impairs POLR3K–POLR3B protein interactions, causes abnormal gut development in zebrafish, and results in a severe decrease (60–80%) in 5S and 7SL ribosomal RNA expression in patient fibroblasts. Homozygosity mapping + whole-exome sequencing in patients, structural analysis, zebrafish gut development assay, RNA analysis of patient fibroblasts Neurology. Genetics Medium 30584594
1998 Human POLR3K (hRPC11) encodes a 108-amino acid protein with a classical Zn-binding motif (CxxCx16-17CxxC) at the N-terminus and a C-terminal domain highly homologous to the zinc ribbon of elongation factor TFIIS, suggesting a role in elongation or termination of RNA synthesis by Pol III. RT-PCR cloning, cDNA sequence analysis, domain homology comparison Bioorganicheskaia khimiia Low 10079944
2025 Modeling the POLR3K-R41W (HLD-associated) mutation in the yeast Rpc11 linker domain (R43W in S. cerevisiae, R41W in S. pombe) demonstrates that this mutation specifically impairs RNA 3' cleavage activity of Pol III without compromising transcription termination; it causes slow growth (especially at low temperatures), lengthening of 3'-oligo(U) sequences in tRNAs, and a fatal phenotype in Sen1-deleted strains. Site-directed mutagenesis in S. cerevisiae and S. pombe, in vitro RNA 3' cleavage assay, termination assay, growth assay, tRNA 3'-oligo(U) length analysis, genetic epistasis with sen1 deletion Biochemical and biophysical research communications High 40651364
2024 A missense variant in POLR3K (c.322G>T; p.D108Y) at the C-terminus is predicted to impair residue interactions and cause steric interference in enzyme conformational changes; a large deletion removing the last exon of POLR3K produces a truncated amorphic protein; both pathogenic variants reduce POLR3K RNA levels and cause selective reduction of specific tRNA species in patient cells, while other Pol III transcripts are unaffected, indicating partial Pol III function. Next-generation sequencing, RNA-level expression analysis in patient-derived cells, structural prediction modeling, tRNA quantification Human mutation Medium 40225923

Source papers

Stage 0 corpus · 29 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 3' processing of eukaryotic precursor tRNAs. Wiley interdisciplinary reviews. RNA 116 21572561
2018 Mutation in POLR3K causes hypomyelinating leukodystrophy and abnormal ribosomal RNA regulation. Neurology. Genetics 72 30584594
2012 TOR signaling regulates ribosome and tRNA synthesis via LAMMER/Clk and GSK-3 family kinases. Molecular cell 70 22364741
2007 Mutation of RNA Pol III subunit rpc2/polr3b Leads to Deficiency of Subunit Rpc11 and disrupts zebrafish digestive development. PLoS biology 61 18044988
2005 Mutations in the RNA polymerase III subunit Rpc11p that decrease RNA 3' cleavage activity increase 3'-terminal oligo(U) length and La-dependent tRNA processing. Molecular and cellular biology 57 15632064
2021 RNA Polymerase III Subunit Mutations in Genetic Diseases. Frontiers in molecular biosciences 55 34395528
2002 Delineation of an estimated 6.7 MB candidate interval for an anophthalmia gene at 3q26.33-q28 and description of the syndrome associated with visible chromosome deletions of this region. European journal of human genetics : EJHG 33 12461687
2011 Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III. Nucleic acids research 32 21450810
2019 Biallelic variants in POLR3GL cause endosteal hyperostosis and oligodontia. European journal of human genetics : EJHG 31 31089205
2019 Novel mutations of the POLR3A gene caused POLR3-related leukodystrophy in a Chinese family: a case report. BMC pediatrics 25 31438894
2014 A methods review on use of nonsense suppression to study 3' end formation and other aspects of tRNA biogenesis. Gene 17 25447915
2006 Ancient origin, functional conservation and fast evolution of DNA-dependent RNA polymerase III. Nucleic acids research 15 16877568
2021 POLR3-related leukodystrophy: How do mutations affecting RNA polymerase III subunits cause hypomyelination? Faculty reviews 12 33659930
2020 Time-resolved RNA-seq provided a new understanding of intestinal immune response of European eel (Anguilla anguilla) following infection with Aeromonas hydrophila. Fish & shellfish immunology 12 32707296
2015 A high density of cis-information terminates RNA Polymerase III on a 2-rail track. RNA biology 10 26636900
2023 Craniofacial features of POLR3-related leukodystrophy caused by biallelic variants in POLR3A, POLR3B and POLR1C. Journal of medical genetics 9 37197783
2009 Predicting functional upstream open reading frames in Saccharomyces cerevisiae. BMC bioinformatics 9 20042076
2017 Characterization of a Large Novel α-Globin Gene Cluster Deletion Causing α0-Thalassemia in a Chinese Family. Hemoglobin 5 29161910
2025 Comprehensive genotype-phenotype analysis in POLR3-related disorders. HGG advances 3 40684265
2024 Novel Pathogenic Variants in POLR3K Cause POLR3-Related Leukodystrophy. Human mutation 3 40225923
2023 The First Case of 4H Syndrome with Type 1 Diabetes Mellitus. Journal of clinical research in pediatric endocrinology 3 36974356
2023 Identification of a novel 91.5 kb-deletion (αα)FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing. The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 3 37673790
2022 The First Korean Siblings With Adult-Onset 4H Leukodystrophy Related to Nonsynonymous POLR3B Mutations. Neurology. Genetics 3 35434302
1998 [Molecular identification and characteristics of hRPC11, the smallest specific subunit of human RNA polymerase III]. Bioorganicheskaia khimiia 2 10079944
2026 Study of POLR3A variants in a family trio suggests mutation-specific pathogenetic mechanisms: insights from integrative OMIC approaches. Cell communication and signaling : CCS 0 41634725
2026 New biomarkers for the detection of fetal death derived from large-scale proteomic analysis of maternal plasma. American journal of obstetrics and gynecology 0 41935727
2026 Identification of novel candidate neural genes for diet-induced obesity in outbred heterogeneous stock rats. Research square 0 42239780
2025 Understanding the molecular basis of the mutation in the RNA polymerase III subunit Rpc10 (R41W)- associated with hypomyelinating leukodystrophy in the yeast homolog Rpc11. Biochemical and biophysical research communications 0 40651364
2025 Investigating the genetic imprint of long body length, high lean meat rate, high fertility and long gestation period in Danish Landrace pigs. BMC genomics 0 41023780

Missed literature

Know a paper Affinage missed for POLR3K? Flag it for the maintainers and the community.

No submissions yet.