Affinage

TPRKB

EKC/KEOPS complex subunit TPRKB · UniProt Q9Y3C4

Length
175 aa
Mass
19.7 kDa
Annotated
2026-06-10
44 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TPRKB (CGI-121) is a core subunit of the conserved eukaryotic KEOPS complex, occupying the terminal position of the linear Gon7–Pcc1–Kae1–Bud32–Cgi121 architecture, where it directly binds and allosterically regulates the kinase/ATPase Bud32 (PRPK) (PMID:18951093, PMID:25735745, PMID:27903914). Within KEOPS, TPRKB is dispensable for the core t6A tRNA-modification catalytic step—the minimal catalytic unit being Pcc1–Kae1–Bud32—but it modulates overall complex activity and, in the holoenzyme, contributes to recruiting and positioning the tRNA substrate for Kae1-catalyzed modification (PMID:23945934, PMID:39639027). Beyond t6A biosynthesis, TPRKB and KEOPS regulate telomere homeostasis: Cgi121 promotes telomeric single-stranded G-overhang generation and telomere recombination/elongation in a manner genetically separable from t6A activity, such that its loss suppresses the cdc13-1 capping defect and extends cellular lifespan (PMID:16564010, PMID:25822194, PMID:29804714). In human cells, TPRKB is stabilized through direct binding by PRPK and is subject to TP53-dependent proteasomal degradation, rendering TP53-deficient cancer cells selectively dependent on TPRKB for proliferation (PMID:31110156). Loss of TPRKB impairs translation, triggers ER stress, DNA-damage signaling and apoptosis, disrupts the actin cytoskeleton, and is essential for mouse development (PMID:28805828, PMID:34849815).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2003 Medium

    Established TPRKB's first molecular partner by identifying it as a direct PRPK-binding protein that modulates PRPK–p53 association, framing it as a regulator of a p53-linked kinase.

    Evidence Yeast two-hybrid, reciprocal co-IP, and recombinant competition assay in human cells

    PMID:12659830

    Open questions at the time
    • Did not place TPRKB within a defined multiprotein complex
    • Functional consequence of inhibiting PRPK–p53 binding in cells not established
  2. 2006 High

    Placed Cgi121/TPRKB into the KEOPS complex and revealed a telomere-maintenance role, showing its deletion suppresses a telomere-capping defect by reducing telomeric ssDNA.

    Evidence Genome-wide suppressor screen and telomere assays in S. cerevisiae

    PMID:16564010

    Open questions at the time
    • Mechanism linking KEOPS to ssDNA/G-overhang generation not defined
    • Relationship between telomere role and any enzymatic activity unknown
  3. 2008 High

    Defined the architecture of KEOPS, showing Cgi121 sits at the terminus of a linear complex and regulates the kinase Bud32, which in turn regulates Kae1.

    Evidence X-ray crystallography of archaeal KEOPS subcomplexes

    PMID:18951093

    Open questions at the time
    • Did not assign a catalytic activity to the complex
    • Human complex composition (e.g., Gon7/LAGE3) not addressed
  4. 2013 High

    Separated TPRKB's role from catalysis, demonstrating it is an allosteric modulator dispensable for the minimal Pcc1–Kae1–Bud32 t6A biosynthesis unit.

    Evidence In vitro reconstitution of t6A activity with defined archaeal subcomplexes

    PMID:23945934

    Open questions at the time
    • Precise allosteric mechanism on complex activity unresolved
    • Whether modulation matters in vivo not tested
  5. 2015 High

    Resolved the PRPK–TPRKB interface and confirmed the linear heteropentameric arrangement, showing Cgi121 caps the C-terminus of Bud32 bound to ADP.

    Evidence X-ray crystallography of Bud32/Cgi121 with ADP and structural modeling

    PMID:25735745

    Open questions at the time
    • Substrate (tRNA) contacts not visualized
    • Conformational changes during catalysis not captured
  6. 2015 Medium

    Mechanistically tied Cgi121 to telomere recombination, showing its loss reduces telomeric ssDNA and extends cellular lifespan in telomerase-positive and -negative cells.

    Evidence Genetic deletion, recombination and lifespan assays in S. cerevisiae

    PMID:25822194

    Open questions at the time
    • Direct biochemical activity generating ssDNA not identified
    • Conservation of telomere role in human cells untested
  7. 2016 Medium

    Confirmed the human KEOPS composition and hinted at functions beyond t6A by mapping subcomplex-specific interactors of TPRKB.

    Evidence AP-MS interactome of all four human KEOPS subunits

    PMID:27903914

    Open questions at the time
    • Functional significance of non-KEOPS interactors unvalidated
    • Direct vs indirect interactions not distinguished
  8. 2017 High

    Defined cellular consequences of TPRKB loss in humans and model organisms—impaired translation, ER stress, DNA-damage signaling, apoptosis, cytoskeletal defects—linking it to a human disease context.

    Evidence siRNA knockdown in human cells/podocytes, CRISPR knockout in zebrafish and mice, multiple functional assays

    PMID:28805828

    Open questions at the time
    • Whether phenotypes derive from t6A loss vs complex-independent roles not dissected
    • Direct cause of cytoskeletal defects unknown
  9. 2018 Medium

    Genetically uncoupled KEOPS telomere function from t6A, showing G-overhang generation persists independently of restored t6A modification.

    Evidence Qri7 complementation, telomere G-overhang analysis, epistasis in yeast

    PMID:29804714

    Open questions at the time
    • Molecular activity driving G-overhang formation unidentified
    • Direct TPRKB-specific contribution vs whole-complex effect unclear
  10. 2019 Medium

    Revealed a complex-independent, synthetic-lethal vulnerability: TP53-deficient cells require TPRKB because TP53 drives its proteasomal degradation, which PRPK binding counteracts.

    Evidence shRNA knockdown, TP53 reintroduction, proteasome inhibition, in vitro/in vivo proliferation, KEOPS-member epistasis

    PMID:31110156

    Open questions at the time
    • Identity of the E3 ligase/intermediary in TP53-dependent degradation unknown
    • Why TP53-null cells depend on TPRKB mechanistically unresolved
  11. 2021 High

    Provided an atomic view of the human PRPK–TPRKB interaction and mapped disease mutations, including one abolishing OSGEP binding.

    Evidence 2.53 Å crystal structure of PRPK–TPRKB–AMPPNP with disease-mutation binding assay

    PMID:33547416

    Open questions at the time
    • Full assembled human holoenzyme not crystallized
    • Functional impact of most mapped mutations untested
  12. 2021 Medium

    Established organismal essentiality by showing Tprkb-null mice are embryonic lethal.

    Evidence i-GONAD CRISPR knockout mouse, embryo survival analysis

    PMID:34849815

    Open questions at the time
    • Developmental stage and tissue of lethality not characterized
    • Mechanism of essential requirement not addressed
  13. 2024 High

    Captured TPRKB in the substrate-engaged holoenzyme, defining KEOPS–tRNA contacts required for Bud32 ATPase regulation and t6A activity.

    Evidence Cryo-EM of KEOPS with and without tRNA plus mutagenesis of contact surfaces

    PMID:39639027

    Open questions at the time
    • TPRKB's direct contribution to tRNA positioning vs scaffolding not fully isolated
    • Dynamics of catalytic cycle not resolved
  14. 2024 Medium

    Identified an upstream regulatory layer in cancer, showing METTL5-mediated m6A stabilizes TPRKB mRNA to drive hepatocellular carcinoma progression.

    Evidence m6A analysis, METTL5/TPRKB knockdown-overexpression epistasis, mRNA stability and tumor assays

    PMID:39182664

    Open questions at the time
    • Downstream effectors of TPRKB driving HCC phenotypes unidentified
    • Whether this acts through KEOPS or complex-independent functions unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The biochemical activity by which TPRKB/KEOPS generates telomeric G-overhangs independently of t6A, and the molecular basis of TP53-dependent TPRKB degradation, remain undefined.
  • No enzyme or activity assigned to G-overhang generation
  • E3 ligase mediating TP53-dependent TPRKB turnover unknown
  • Mechanistic basis of TP53-deficient synthetic lethality unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 3 GO:0003723 RNA binding 1
Localization
GO:0005634 nucleus 1 GO:0005829 cytosol 1
Pathway
R-HSA-392499 Metabolism of proteins 2 R-HSA-8953854 Metabolism of RNA 2
Partners
LAGE3OSGEPTP53TP53RK
Complex memberships
KEOPS/EKC complex

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2003 TPRKB (CGI-121) was identified as a direct binding partner of PRPK (TP53RK) via yeast two-hybrid screening, and the interaction was confirmed in vivo and in vitro. TPRKB localizes to both nucleus and cytosol. Recombinant TPRKB inhibited co-precipitation of p53 by recombinant PRPK in vitro, suggesting TPRKB acts as an inhibitor of PRPK-p53 binding. Yeast two-hybrid, co-immunoprecipitation in vivo and in vitro, immunocytochemistry, recombinant protein competition assay Biochemical and biophysical research communications Medium 12659830
2006 TPRKB (CGI-121/Cgi121 in yeast) is a subunit of the conserved KEOPS complex (with Kae1, Bud32/PRPK, and Pcc1). Deletion of CGI121 suppresses the cdc13-1 telomere-capping defect by dramatically reducing ssDNA accumulation at telomeres. KEOPS components including Cgi121 are required for telomere elongation and de novo telomere addition to DNA double-strand breaks. Genome-wide suppressor screen (S. cerevisiae), genetic deletion, telomere length assays, epistasis analysis Cell High 16564010
2008 The atomic structure of archaea-derived KEOPS complexes (Kae1, Bud32, Pcc1, Cgi121) was solved, revealing that Cgi121 regulates the primordial kinase Bud32, which in turn regulates Kae1. Structural analysis indicates Cgi121 sits at the terminus of a linear complex arrangement. X-ray crystallography of archaeal KEOPS complex Molecular cell High 18951093
2013 Within the KEOPS/EKC complex, Cgi121 (TPRKB ortholog) acts as an allosteric regulator of the minimal functional unit (Pcc1-Kae1-Bud32). Cgi121 is not required for the core t6A biosynthesis catalytic step but modulates the complex activity. The minimal unit for t6A synthesis is Pcc1-Kae1-Bud32. Reconstitution of t6A biosynthesis activity with subcomplexes, biochemical assays in archaeal system Nucleic acids research High 23945934
2015 Crystal structure of the Bud32/Cgi121 (PRPK/TPRKB) subcomplex with ADP revealed that ADP binds in the catalytic site of Bud32 in a canonical PKA-family manner, and Cgi121 caps the C-terminal end of Bud32. The yeast KEOPS complex exists as a heteropentamer in a linear arrangement: Gon7-Pcc1-Kae1-Bud32-Cgi121. X-ray crystallography of Bud32/Cgi121 complex with ADP, structural modeling Nucleic acids research High 25735745
2015 In S. cerevisiae, inactivation of KEOPS subunit Cgi121 (TPRKB ortholog) specifically inhibits telomere recombination. Deletion of CGI121 reduced telomeric ssDNA generation, consistent with Cgi121 promoting ssDNA at telomeres to enable recombination. This inhibition of telomere recombination significantly extended cellular lifespan in both telomerase-positive and telomerase-negative cells. Genetic deletion, telomere recombination assays, lifespan analysis, epistasis with yku80 mutant PLoS genetics Medium 25822194
2016 Proteomic analysis of human KEOPS confirmed TPRKB as a core subunit interacting with OSGEP (Kae1), TP53RK (Bud32/PRPK), and LAGE3 (Pcc1). Mass spectrometry identified 152 protein interactors; specific interactors were found for different KEOPS subcomplexes, suggesting TPRKB may have functions outside of t6A biosynthesis. Affinity purification mass spectrometry (AP-MS), proteomic interactome analysis of human KEOPS Nucleic acids research Medium 27903914
2017 Knockdown of TPRKB in human cells inhibited cell proliferation, impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and induced apoptosis. Knockdown also induced defects in the actin cytoskeleton and decreased migration rate of human podocytes. Human disease mutations in TPRKB did not rescue these proliferation defects. siRNA knockdown in human cell lines and podocytes, CRISPR-Cas9 knockout in zebrafish and mice, cell proliferation assays, actin cytoskeleton imaging, migration assays Nature genetics High 28805828
2018 Telomere length regulation by the KEOPS complex (including Cgi121/TPRKB) is independent of its t6A biosynthesis activity. Cytoplasmic overexpression of Qri7 (mitochondrial Kae1 ortholog) restored t6A modification and cell growth but failed to rescue telomere length in kae1Δ cells. KEOPS subunit deletions cause dramatic reduction in telomeric G-overhang, indicating KEOPS promotes G-overhang generation for telomere length regulation. Yeast genetics, Qri7 complementation experiments, in vitro biochemical assays, telomere G-overhang analysis, genetic epistasis Journal of genetics and genomics Medium 29804714
2019 TPRKB knockdown selectively inhibits proliferation of TP53-deficient cancer cells but has minimal effect in TP53 wild-type cells. TP53 reintroduction into TP53-null cells rescued sensitivity to TPRKB knockdown. TP53 indirectly mediates TPRKB protein degradation (via proteasome), and this degradation was rescued by co-expression of PRPK (TP53RK) or by proteasome inhibition. Depletion of other EKC/KEOPS members showed TP53-independent effects, supporting a complex-independent function for TPRKB. shRNA knockdown, in vitro and in vivo proliferation assays, TP53 reintroduction, proteasome inhibition, epistasis with other KEOPS members Molecular cancer research Medium 31110156
2021 The 2.53 Å crystal structure of the human PRPK-TPRKB-AMPPNP complex was solved. The structure reveals details of PRPK-AMPPNP nucleotide coordination and the PRPK-TPRKB protein-protein interaction interface. PRPK appears in an active conformation despite lacking a conventional kinase activation loop. Disease mutations in PRPK and TPRKB were mapped onto the structure; one mutation, PRPK K238Nfs*2, was shown experimentally to abolish binding to OSGEP. X-ray crystallography (2.53 Å), structural modeling of full human KEOPS, binding assay for disease mutation Communications biology High 33547416
2021 Generation of the first Tprkb null knockout mouse strain demonstrated embryonic lethality, establishing that TPRKB is essential for mouse development. i-GONAD CRISPR knockout in mice, survival analysis of homozygous null embryos G3 (Bethesda, Md.) Medium 34849815
2024 Cryo-EM structures of the full KEOPS complex with and without tRNA substrate revealed that Cgi121 (TPRKB) is part of the holo-enzyme substrate complex. The structures uncovered contact surfaces within KEOPS-tRNA required for Bud32 ATPase regulation and t6A modification activity. Cgi121's position at the terminus of the linear complex contributes to tRNA binding and positioning for Kae1-catalyzed modification. Cryo-electron microscopy (cryo-EM) of KEOPS with and without tRNA, mutagenesis of contact surfaces Nature communications High 39639027
2024 METTL5 positively regulates TPRKB mRNA stability through N6-methyladenosine (m6A) modification, thereby enhancing TPRKB protein expression in hepatocellular carcinoma cells. TPRKB knockdown suppressed HCC cell viability, colony formation, invasion, migration, and tumor growth in vivo. TPRKB overexpression partially rescued the anti-cancer effects of METTL5 knockdown. m6A modification analysis, METTL5 knockdown/overexpression, TPRKB knockdown/overexpression, mRNA stability assay, in vitro and in vivo tumor assays Experimental cell research Medium 39182664

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly. Nature genetics 173 28805828
2006 A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 152 16564010
2008 Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine. Molecular cell 83 18951093
2013 Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system. Nucleic acids research 67 23620299
2013 Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. Nucleic acids research 64 23945934
2016 Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7. Nucleic acids research 56 27903914
2014 Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue. Neurogenetics 41 24659297
2015 Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex. Nucleic acids research 38 25735745
2021 The structural and functional workings of KEOPS. Nucleic acids research 33 34614169
2016 Structural and functional characterization of KEOPS dimerization by Pcc1 and its role in t6A biosynthesis. Nucleic acids research 25 27302132
2012 A genetic investigation of the KEOPS complex in halophilic Archaea. PloS one 22 22927945
2019 Novel homozygous OSGEP gene pathogenic variants in two unrelated patients with Galloway-Mowat syndrome: case report and review of the literature. BMC nephrology 21 30975089
2003 Identification of CGI-121, a novel PRPK (p53-related protein kinase)-binding protein. Biochemical and biophysical research communications 20 12659830
2015 Inhibition of telomere recombination by inactivation of KEOPS subunit Cgi121 promotes cell longevity. PLoS genetics 19 25822194
2018 Acute multi-sgRNA knockdown of KEOPS complex genes reproduces the microcephaly phenotype of the stable knockout zebrafish model. PloS one 18 29346415
2018 Yeast KEOPS complex regulates telomere length independently of its t6A modification function. Journal of genetics and genomics = Yi chuan xue bao 18 29804714
2013 The Drosophila EKC/KEOPS complex: roles in protein synthesis homeostasis and animal growth. Fly 18 23823807
2021 The utility of next-generation sequencing technologies in diagnosis of Mendelian mitochondrial diseases and reflections on clinical spectrum. Journal of pediatric endocrinology & metabolism : JPEM 15 33629572
2018 A familial case of Galloway-Mowat syndrome due to a novel TP53RK mutation: a case report. BMC medical genetics 15 30053862
2021 Crystal structure of the human PRPK-TPRKB complex. Communications biology 14 33547416
2019 Identification of TP53RK-Binding Protein (TPRKB) Dependency in TP53-Deficient Cancers. Molecular cancer research : MCR 13 31110156
2018 Nephrological and urological complications of homozygous c.974G>A (p.Arg325Gln) OSGEP mutations. Pediatric nephrology (Berlin, Germany) 11 30141175
2014 Kinase-associated endopeptidase 1 (Kae1) participates in an atypical ribosome-associated complex in the apicoplast of Plasmodium falciparum. The Journal of biological chemistry 11 25204654
2024 METTL5 enhances the mRNA stability of TPRKB through m6A modification to facilitate the aggressive phenotypes of hepatocellular carcinoma cell. Experimental cell research 9 39182664
2006 Identification of differentially expressed genes induced by angiotensin II in rat cardiac fibroblasts. Clinical and experimental pharmacology & physiology 9 16445697
2023 Diagnosis delay a family of Galloway-Mowat Syndrome caused by a classical splicing mutation of Lage3. BMC nephrology 7 36755238
2022 Unraveling the Pathobiological Role of the Fungal KEOPS Complex in Cryptococcus neoformans. mBio 7 36377896
2021 Galloway-Mowat syndrome: New insights from bioinformatics and expression during Xenopus embryogenesis. Gene expression patterns : GEP 6 34619372
2024 Ganoderic acid A ameliorates depressive-like behaviors in CSDS mice: Insights from proteomic profiling and molecular mechanisms. Journal of affective disorders 5 38723681
2023 A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea. Nature communications 5 36720870
2023 Sua5 catalyzing universal t6A tRNA modification is responsible for multifaceted functions of the KEOPS complex in Cryptococcus neoformans. mSphere 5 38085018
2023 The archaeal KEOPS complex possesses a functional Gon7 homolog and has an essential function independent of the cellular t6A modification level. mLife 5 38818338
2020 KEOPS complex expression in the frontal cortex in major depression and schizophrenia. The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry 5 32914678
2024 Case Report: Novel compound heterozygous TPRKB variants cause Galloway-Mowat syndrome. Frontiers in pediatrics 3 38628357
2024 Structures of KEOPS bound to tRNA reveal functional roles of the kinase Bud32. Nature communications 3 39639027
2022 Kae1 of Saccharomyces cerevisiae KEOPS complex possesses ADP/GDP nucleotidase activity. The Biochemical journal 3 36416748
2021 An efficient i-GONAD method for creating and maintaining lethal mutant mice using an inversion balancer identified from the C3H/HeJJcl strain. G3 (Bethesda, Md.) 3 34849815
2023 Novel LAGE3 Pathogenic Variants Combined with TRPC6 and NUP160 Variants in Galloway-Mowat Syndrome: A Case Report. Case reports in nephrology and dialysis 2 37900929
2025 Genetics and phenotypic heterogeneity of Galloway-Mowat syndrome. Cell communication and signaling : CCS 1 40533795
2023 Evidence of polygenic regulation of the physiological presence of neurofilament light chain in human serum. Frontiers in neurology 1 36970523
2022 A suite of in vitro and in vivo assays for monitoring the activity of the pseudokinase Bud32. Methods in enzymology 1 35525560
2026 Significance of Methyltransferase-like 5 Expression in Oral Squamous Cell Carcinoma. International dental journal 0 42019204
2025 Multi-omics analysis identifies OSGEPL1 as an oncogene in hepatocellular carcinoma. Discover oncology 0 40090949
2021 Reciprocal hemizygosity analysis reveals that the Saccharomyces cerevisiae CGI121 gene affects lag time duration in synthetic grape must. G3 (Bethesda, Md.) 0 33681985

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