Affinage

RPP38

Ribonuclease P protein subunit p38 · UniProt P78345

Length
283 aa
Mass
31.8 kDa
Annotated
2026-06-10
32 papers in source corpus 17 papers cited in narrative 17 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RPP38 (p38/Th40) is a shared protein subunit of the human RNase P and RNase MRP ribonucleoprotein endonucleases, required for normal processing of tRNA precursors (PMID:9037013, PMID:10199568, PMID:12907726). It was first isolated as one of several polypeptides copurifying with catalytically active RNase P and is a target of scleroderma autoimmune sera; antibodies against it immunoprecipitate active holoenzyme, establishing it as a genuine subunit (PMID:9037013, PMID:9630247). RPP38 directly binds the RNA subunit of RNase P (H1 RNA) and also associates with RNase MRP RNA, integrating into both complexes through multiple weak protein-protein contacts within a loosely assembled protein core (PMID:10199568, PMID:11455963, PMID:15096576, PMID:11158571). Structural studies of its archaeal homologue show that RPP38 belongs to the L7Ae/L30e fold family and recognizes K-turn motifs in the RNase P/MRP RNA via a defined set of contact residues (PMID:27114305, PMID:29372908). It localizes uniformly throughout the nucleolus, directed by an intrinsic basic domain that targets it to nucleoli independently of complex assembly (PMID:10444065, PMID:11694598). Functionally, knockdown of RPP38 causes accumulation of tRNA precursors, reduces RNase P activity in vitro, and coordinately lowers the levels of a subset of other RNase P protein subunits without affecting H1 RNA, indicating co-regulated expression of these subunits (PMID:12907726, PMID:12552092). Unlike the RNase P subunits Rpp29 and Rpp21, RPP38 is not recruited to sites of DNA damage (PMID:28432356).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1997 High

    Established that a 38 kDa polypeptide is a bona fide component of human RNase P, defining the protein composition of a previously RNA-centric enzyme.

    Evidence 2000-fold biochemical purification of RNase P from HeLa cells with scleroderma serum immunodepletion, peptide sequencing, and cDNA cloning

    PMID:9037013

    Open questions at the time
    • Copurification alone did not prove direct association with the active enzyme
    • No RNA- or protein-binding partners identified
  2. 1998 High

    Confirmed Rpp38 is an integral subunit of the catalytically active holoenzyme rather than a copurifying contaminant.

    Evidence Recombinant-protein-derived polyclonal antibodies immunoprecipitating active RNase P holoenzyme

    PMID:9630247

    Open questions at the time
    • Did not define which RNA or proteins Rpp38 contacts within the complex
  3. 1999 High

    Showed Rpp38 is shared between RNase P and RNase MRP and defined its nucleolar localization, linking it to two distinct processing enzymes.

    Evidence VSV-tagged co-immunoprecipitation of both complexes, UV crosslinking to MRP RNA nt 86-176, and immunofluorescence with a nucleolar-targeting reporter assay

    PMID:10199568 PMID:10444065

    Open questions at the time
    • Did not identify the molecular determinant of complex selectivity
    • Distinct from Rpp14/Rpp29 dense-fibrillar-component localization, but functional meaning unresolved
  4. 2001 High

    Mapped Rpp38's molecular contacts—direct binding to H1 RNA and weak protein-protein interactions—and localized its nucleolar-targeting basic domain, building the architecture of the particle.

    Evidence Yeast three-hybrid and UV crosslinking for H1 RNA binding; yeast two-hybrid for inter-subunit contacts; GFP deletion mutants and co-IP for the basic nucleolar domain

    PMID:11158571 PMID:11455963 PMID:11694598

    Open questions at the time
    • Two-hybrid interactions were weak and not all reciprocally validated
    • Nucleolar targeting independent of complex association left functional rationale open
  5. 2002 High

    Resolved the identity of the Th40 autoantigen as Rpp38 and corrected the prior assignment that Rpp38 binds the MRP P3 domain.

    Evidence Reconstitution and UV crosslinking with recombinant proteins and patient antisera

    PMID:12483731

    Open questions at the time
    • The precise MRP RNA element bound by Rpp38 within the complex remained to be pinned down
  6. 2003 Medium

    Demonstrated a functional requirement for Rpp38 in tRNA precursor processing and uncovered coordinate co-regulation of a subset of RNase P protein subunits.

    Evidence Stable overexpression, siRNA and EGS knockdown in HeLa cells with Northern blotting, in vitro RNase P activity assays, and RT-PCR/immunoblotting of other subunits

    PMID:12552092 PMID:12907726

    Open questions at the time
    • Mechanism of coordinate subunit co-regulation not defined
    • Whether processing defects are direct or secondary to subunit depletion unresolved
  7. 2004 Medium

    Placed Rpp38 within an interaction map of the RNase MRP RNP, showing it directly binds both MRP RNA and multiple protein subunits.

    Evidence GST pull-down assays with recombinant subunits and MRP RNA fragment/deletion mutants

    PMID:15096576

    Open questions at the time
    • Pull-down interactions not confirmed in the assembled holoenzyme
    • Stoichiometry and spatial arrangement not determined
  8. 2006 Medium

    Refined the picture of Rpp38 distribution across MRP complex states and the co-regulated subunit set.

    Evidence Glycerol gradient sedimentation and VSV-tagged co-IP across 12S and 60-80S MRP complexes; inducible EGS knockdown system

    PMID:16131590 PMID:16723659

    Open questions at the time
    • Functional difference between 12S and larger MRP complexes for Rpp38 unclear
  9. 2016 High

    Provided atomic-level mechanism for how Rpp38 recognizes its RNA target by solving the archaeal homologue bound to a K-turn motif.

    Evidence X-ray crystallography of PhoRpp38–SL12M (3.4 Å) with structure-based mutagenesis and pull-down validation

    PMID:27114305

    Open questions at the time
    • Structure is of the archaeal homologue, not human RPP38
    • K-turn binding by human RPP38 within its complexes not directly co-crystallized
  10. 2017 Medium

    Distinguished Rpp38 from other RNase P subunits in moonlighting function by showing it is not recruited to DNA damage sites.

    Evidence Live-cell laser microirradiation imaging (negative result for Rpp38)

    PMID:28432356

    Open questions at the time
    • Does not exclude DNA-damage roles under other conditions
    • Negative result for a single recruitment readout
  11. 2018 High

    Extended the structural basis of K-turn recognition and demonstrated Rpp38 assembly with neighboring subunits on an extended RNA stem-loop.

    Evidence Higher-resolution X-ray structures of PhoRpp38–K-turn complexes (2.1 Å, 3.1 Å) and co-purification of PhoRpp38/Rpp21/Rpp29 with P10-P12.2 RNA

    PMID:29372908

    Open questions at the time
    • Archaeal system; human subassembly architecture not directly resolved
    • Catalytic contribution of Rpp38 to substrate cleavage not addressed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RPP38-mediated K-turn recognition is integrated into substrate selection and catalysis by the human RNase P and MRP holoenzymes, and the mechanism of coordinate co-regulation of RNase P subunits, remain unresolved.
  • No human RPP38–RNA structure within the assembled holoenzyme
  • Mechanism linking RPP38 depletion to loss of other subunits unknown
  • Functional partition of RPP38 between RNase P and MRP roles undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 5
Localization
GO:0005730 nucleolus 2
Pathway
R-HSA-8953854 Metabolism of RNA 3
Partners
POP1RPP20RPP21RPP25RPP29RPP30RPP40
Complex memberships
RNase MRPRNase P

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1997 RPP38 (p38) was identified as a protein subunit of human RNase P that copurifies with the enzyme activity from HeLa cells; it is one of six polypeptides (14, 20, 25, 30, 38, 40 kDa) that copurify with RNase P, and scleroderma autoimmune sera that immunodeplete RNase P activity react specifically with p38 on immunoblots. 2000-fold purification of human RNase P from HeLa cells, immunodepletion with scleroderma sera, immunoblotting, peptide sequencing, cDNA cloning Proceedings of the National Academy of Sciences of the United States of America High 9037013
1998 Polyclonal antibodies raised against recombinant Rpp38 recognize the corresponding protein associated with purified RNase P and precipitate catalytically active holoenzyme, confirming Rpp38 is a genuine subunit of the active RNase P complex. Recombinant protein production, polyclonal antibody generation, immunoprecipitation of active holoenzyme, immunoblotting RNA (New York, N.Y.) High 9630247
1999 Rpp38 is localized to the nucleolus, where it is uniformly distributed (unlike Rpp14 and Rpp29 which are confined to the dense fibrillar component). Rpp38 possesses a functional domain required for subnucleolar localization and can localize a reporter protein to nucleoli. Immunofluorescence microscopy, reporter protein localization assay in cultured cells, biochemical fractionation The Journal of cell biology High 10444065
1999 Rpp38 is associated with the RNase MRP complex as well as RNase P. VSV-tagged Rpp38 expressed in HeLa cells co-immunoprecipitates both RNase P and RNase MRP complexes. UV crosslinking followed by anti-Rpp38 immunoprecipitation identified Rpp38 as the ~40 kDa protein that associates with the central part of MRP RNA (nt 86-176). VSV-epitope tagging, immunoprecipitation in HeLa cells, UV crosslinking followed by immunoprecipitation with anti-Rpp38 antibodies RNA (New York, N.Y.) High 10199568
2001 Rpp38 participates in protein-protein interactions within the human nuclear RNase P holoenzyme complex, as detected by yeast two-hybrid analysis. These interactions are weak, consistent with a loosely assembled protein core. Yeast two-hybrid system using protein subunits of human nuclear RNase P Proceedings of the National Academy of Sciences of the United States of America Medium 11158571
2001 Rpp38 directly interacts with H1 RNA, the RNA subunit of human nuclear RNase P, as demonstrated by yeast three-hybrid assay and confirmed by UV crosslinking of the purified holoenzyme. Yeast three-hybrid system, UV crosslinking of purified RNase P holoenzyme RNA (New York, N.Y.) High 11455963
2001 A basic domain in Rpp38 is responsible for its nucleolar accumulation, and Rpp38 can accumulate in the nucleolus independently of its association with the RNase MRP and RNase P complexes. A deletion mutant of Rpp38 was identified that preferentially associates with the RNase MRP complex rather than RNase P, providing a clue about differences in protein composition between the two complexes. Transfection of GFP-tagged deletion mutants, fluorescence microscopy, co-immunoprecipitation Molecular biology of the cell High 11694598
2002 The previously defined Th40 autoantigen is identical to Rpp38. Reconstitution and UV crosslinking experiments showed that Rpp38 does NOT directly bind to the P3 domain of RNase MRP RNA; the previously reported 40 kDa species associating with the P3 domain appeared to consist of Rpp20 and/or Rpp25. Reconstitution experiments, UV crosslinking, immunoprecipitation with patient antisera and recombinant proteins Arthritis and rheumatism High 12483731
2003 Constitutive overexpression of exogenous tagged Rpp38 in HeLa cells impairs processing of tRNA precursors and affects cleavage and steady-state levels of the 3' ITS1 of rRNA. RNase P purified from these cells shows reduced activity in vitro. Inhibition of Rpp38 by siRNA causes accumulation of the initiator methionine tRNA precursor. Knockdown of Rpp38 coordinately inhibits expression of other RNase P protein subunits (but not H1 RNA). Stable transfection in HeLa cells, Northern blotting for tRNA precursors, in vitro RNase P activity assay, siRNA knockdown Nucleic acids research High 12907726
2003 Targeted inhibition of Rpp38 expression using an external guide sequence (EGS) reduces both Rpp38 mRNA and protein levels within 24 hours. This also coordinately inhibits four other RNase P protein subunits and their mRNAs, without affecting the remaining subunits or H1 RNA, suggesting co-regulated expression of a subset of RNase P protein genes. EGS technology (external guide sequence targeting Rpp38 mRNA), transient transfection, RT-PCR, immunoblotting Proceedings of the National Academy of Sciences of the United States of America Medium 12552092
2004 In the human RNase MRP complex, Rpp38 directly interacts with multiple protein subunits (total of 19 direct protein-protein interactions were mapped among all subunits) and directly binds to RNase MRP RNA, contributing to a model of ribonucleoprotein particle architecture. GST pull-down experiments with recombinant proteins and MRP RNA fragments including deletion mutants Nucleic acids research Medium 15096576
2005 A regulatable EGS targeting Rpp38 stably integrated into a human cell line effectively reduces Rpp38 protein levels upon induction, and also inhibits several other (but not all) RNase P protein subunits at both mRNA and protein levels. Stably integrated inducible pol III promoter system, EGS targeting Rpp38, immunoblotting, RT-PCR RNA (New York, N.Y.) Medium 16131590
2006 Rpp38 (along with hPop1, Rpp40, and Rpp30) is associated with both the 12S and the 60-80S RNase MRP complexes, whereas some other subunits are restricted to 12S. Co-immunoprecipitation with VSV-tagged subunits confirmed that Rpp38 is associated with RNase MRP complexes. Glycerol gradient sedimentation, co-immunoprecipitation with VSV-epitope-tagged protein subunits RNA (New York, N.Y.) Medium 16723659
2006 Computational analysis suggests that the yeast RNase P/MRP protein Pop3p has the same L7Ae/L30e RNA-binding fold as human Rpp38, and that a K-turn motif in RNase P/MRP RNAs may serve as a binding site for Pop3p/Rpp38 proteins. Profile-based computational searches, phylogenetic analysis, structural prediction Nucleic acids research Low 16998185
2016 Crystal structure of the archaeal Rpp38 homologue PhoRpp38 (from Pyrococcus horikoshii) in complex with a K-turn-containing RNA stem-loop (SL12M) was determined at 3.4 Å resolution. Key residues Lys35, Asn38, Glu39, Lys42 interact with G·A and A·G pairs in the K-turn, while Ile93, Glu94, Val95 contact the 3-nucleotide bulge. Structure-based mutagenesis confirmed that the same residues mediate binding to both SL12 and SL16 K-turns in PhoRpp38 RNA. X-ray crystallography (3.4 Å), structure-based mutagenesis, pull-down assay Biochemical and biophysical research communications High 27114305
2017 Rpp38 was explicitly tested and found NOT to be recruited to laser-microirradiated DNA damage sites, in contrast to Rpp29 and Rpp21 which are recruited and play a role in homology-directed repair of double-strand breaks. Live-cell laser microirradiation, fluorescence microscopy (negative result for Rpp38 recruitment) Scientific reports Medium 28432356
2018 Improved crystal structures of archaeal Rpp38 homologue PhoRpp38 in complex with K-turn motifs were determined at 2.1 Å (P12.2) and 3.1 Å (P12.1) resolution. Additional contact residues (Thr37, Asp59, Lys84, Ala96, Ala98) interacting with the three-nucleotide bulge were identified. PhoRpp38 with PhoRpp21 and PhoRpp29 was co-purified with an extended stem-loop containing P10-P12.2. X-ray crystallography (2.1 Å and 3.1 Å), affinity purification of multi-protein RNA complex Acta crystallographica. Section F, Structural biology communications High 29372908

Source papers

Stage 0 corpus · 32 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1997 Characterization of two scleroderma autoimmune antigens that copurify with human ribonuclease P. Proceedings of the National Academy of Sciences of the United States of America 97 9037013
2004 Mutual interactions between subunits of the human RNase MRP ribonucleoprotein complex. Nucleic acids research 86 15096576
1999 Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P. The Journal of cell biology 77 10444065
2006 Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucleic acids research 60 16998185
1999 RNA-protein interactions in the human RNase MRP ribonucleoprotein complex. RNA (New York, N.Y.) 60 10199568
1998 Autoantigenic properties of some protein subunits of catalytically active complexes of human ribonuclease P. RNA (New York, N.Y.) 52 9630247
2001 Protein-protein interactions with subunits of human nuclear RNase P. Proceedings of the National Academy of Sciences of the United States of America 51 11158571
2002 Identity of the RNase MRP- and RNase P-associated Th/To autoantigen. Arthritis and rheumatism 50 12483731
2000 Architecture and function of the human endonucleases RNase P and RNase MRP. IUBMB life 50 10995027
2001 Protein-RNA interactions in the subunits of human nuclear RNase P. RNA (New York, N.Y.) 48 11455963
1999 Rpp14 and Rpp29, two protein subunits of human ribonuclease P. RNA (New York, N.Y.) 48 10024167
2002 Purification and characterization of Rpp25, an RNA-binding protein subunit of human ribonuclease P. RNA (New York, N.Y.) 47 12003489
2002 Differences in autoantibody response to Th/To between systemic sclerosis and other autoimmune diseases. Annals of the rheumatic diseases 46 12176814
2006 Differential association of protein subunits with the human RNase MRP and RNase P complexes. RNA (New York, N.Y.) 44 16723659
2014 Autoantibodies to the mitochondrial RNA processing (MRP) complex also known as Th/To autoantigen. Autoimmunity reviews 29 25462581
2017 A role of human RNase P subunits, Rpp29 and Rpp21, in homology directed-repair of double-strand breaks. Scientific reports 26 28432356
2020 Pilot study of combined aerobic and resistance exercise on fatigue for patients with head and neck cancer: Inflammatory and epigenetic changes. Brain, behavior, and immunity 24 32330594
1999 Construction and characterization of a H19 epitope point mutant of MDV CVI988/Rispens strain. Acta virologica 19 10696440
2001 Basic domains target protein subunits of the RNase MRP complex to the nucleolus independently of complex association. Molecular biology of the cell 18 11694598
2004 Inhibition of the expression of the human RNase P protein subunits Rpp21, Rpp25, Rpp29 by external guide sequences (EGSs) and siRNA. Journal of molecular biology 16 15351636
2016 Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38. Biochemical and biophysical research communications 13 27114305
2003 Coordinate inhibition of expression of several genes for protein subunits of human nuclear RNase P. Proceedings of the National Academy of Sciences of the United States of America 13 12552092
2004 Analyzing the H19- and T65-epitopes in 38 kd phosphorylated protein of Marek's disease viruses and comparing chicken immunological reactions to viruses point-mutated in the epitopes. Science in China. Series C, Life sciences 11 15382680
2012 Pathway analysis of genome-wide association study for bone mineral density. Molecular biology reports 9 22531938
2004 3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p. RNA (New York, N.Y.) 9 15613537
2018 Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif. Acta crystallographica. Section F, Structural biology communications 8 29372908
2019 Autoantibodies to a novel Rpp38 (Th/To) derived B-cell epitope are specific for systemic sclerosis and associate with a distinct clinical phenotype. Rheumatology (Oxford, England) 7 31323671
2011 Assembly of the complex between archaeal RNase P proteins RPP30 and Pop5. Archaea (Vancouver, B.C.) 7 22162665
2003 Alterations in the intracellular level of a protein subunit of human RNase P affect processing of tRNA precursors. Nucleic acids research 7 12907726
2005 Regulated expression of functional external guide sequences in mammalian cells using a U6 RNA polymerase III promoter. RNA (New York, N.Y.) 4 16131590
2025 Ribonuclease P/MRP subunit RPP40 coordinates the transcription of pre-rRNA and ribosomal protein genes to promote Hepatocellular carcinoma malignancy. Gene 1 40517827
2019 Genetic Switches between Cancer and Emphysema Resolution of Cigarette-Smoke Induced Inflammation. EC pulmonology and respiratory medicine 1 38116482

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