Affinage

POP4

Ribonuclease P protein subunit p29 · UniProt O95707

Length
220 aa
Mass
25.4 kDa
Annotated
2026-06-10
15 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 4/4 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

POP4/Rpp29 is a core protein subunit of the human RNase P ribonucleoprotein endonuclease that drives 5'-leader cleavage of precursor tRNAs (PMID:10024167, PMID:18929577). It adopts an OB-fold beta-barrel with flexible N- and C-terminal extensions and contacts the RNase P RNA subunit (PMID:14673079, PMID:18929577). Functionally it acts as a heterodimer with Rpp21, whose assembly is driven by binding-coupled protein folding at the interface (PMID:22243443); within this pair, Rpp21 supplies the primary positively charged RNA-binding surface while Rpp29's C-terminal residues are required for activation, and together they bind and stabilize the specificity (S) domain of the catalytic RNA to license pre-tRNA cleavage (PMID:19733182, PMID:27810361). Beyond tRNA processing, Rpp29 has acquired eukaryote-specific roles: it is recruited to DNA double-strand break sites in a PARP1-dependent manner through poly(ADP-ribose) binding and is required for homology-directed repair but not non-homologous end joining (PMID:28432356), and it directly binds histone H3.3 through its eukaryote-specific N-terminal extension to repress H3.3 nucleosome deposition at active genes and to shape histone modification states (PMID:26842893, PMID:29921582).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1999 Medium

    Established that Rpp29/POP4 is a bona fide protein subunit of the catalytically active human RNase P holoenzyme, not merely an associated factor.

    Evidence cDNA cloning and immunoprecipitation of active RNase P from HeLa cells with anti-Rpp29 antibodies

    PMID:10024167

    Open questions at the time
    • Did not define the structure or RNA-contacting surface of Rpp29
    • No mechanistic role in catalysis assigned
  2. 2003 High

    Defined the fold of Rpp29 as an OB-fold beta-barrel with flexible terminal extensions and showed it is an essential, RNA-contacting subunit, providing the structural framework for its function.

    Evidence Solution/multidimensional NMR structures of archaeal Rpp29 homologs (Mth11, A. fulgidus), reconstitution, and chemical shift perturbation RNA mapping

    PMID:14622001 PMID:14673079

    Open questions at the time
    • Used archaeal homologs rather than human Rpp29
    • Specific RNA contact residues not yet validated by mutagenesis
  3. 2004 High

    Identified candidate RNA-binding surfaces on the Rpp29 OB-fold by crystallography and linked the fold to known RNA-binding proteins.

    Evidence 2.0 Å X-ray structure of archaeal Ph1771p with structural comparison and sulfate-ion binding analysis

    PMID:15317976

    Open questions at the time
    • RNA-binding sites inferred from charge/conservation, not demonstrated functionally
    • Archaeal homolog only
  4. 2008 High

    Showed that Rpp21-Rpp29 heterodimerization plus the catalytic H1 RNA is sufficient to reconstitute pre-tRNA cleavage and resolved the atomic interface of the heterodimer.

    Evidence Crystal structure of archaeal PhoRpp21-PhoRpp29 complex, NMR of RPP21, mutational analysis, and in vitro cleavage reconstitution

    PMID:18922021 PMID:18929577

    Open questions at the time
    • Did not localize the heterodimer on the RNA subunit
    • Thermodynamics of assembly unresolved
  5. 2009 High

    Localized the Rpp21-Rpp29 heterodimer to the specificity (S) domain of the RNase P RNA, defining where the pair acts on the catalytic RNA.

    Evidence Solution NMR structure of the P. furiosus RPP21-RPP29 complex with enzymatic footprinting and chemical shift perturbation

    PMID:19733182

    Open questions at the time
    • Functional partition of S- vs C-domain roles between subunit pairs not yet tested
    • Human complex not directly mapped
  6. 2010 Medium

    Demonstrated functional division of labor in which the Rpp21-Rpp29 pair stabilizes/activates the S-domain while Pop5-Rpp30 acts on the C-domain.

    Evidence Chimeric C/S-domain RNase P RNAs reconstituted with purified archaeal protein subunits and activity assays

    PMID:20139629

    Open questions at the time
    • Single lab, archaeal system
    • Residue-level basis of activation not yet defined
  7. 2012 High

    Established that Rpp29-Rpp21 complex formation is driven by binding-coupled protein folding, explaining the thermodynamics of assembly.

    Evidence Isothermal titration calorimetry with salt/pH dependence, NMR, and a folding-deficient RPP21 mutant

    PMID:22243443

    Open questions at the time
    • Did not address human complex folding kinetics in vivo
    • No link to assembly chaperones
  8. 2016 Medium

    Refined the RNA-activation mechanism by showing Rpp21 supplies the primary RNA-binding surface while specific Rpp29 C-terminal residues are essential for S-domain activation.

    Evidence Pull-down RNA-binding assays, site-directed mutagenesis of PhoRpp21/PhoRpp29, and activity assays with PhopRNA deletion mutants

    PMID:27810361

    Open questions at the time
    • Archaeal system; human residue requirements not confirmed
    • Single lab
  9. 2016 High

    Revealed a moonlighting role for Rpp29 in DNA double-strand break repair, linking RNase P subunits to PARP1-dependent genome maintenance.

    Evidence Laser microirradiation live imaging, PAR-binding assays, siRNA knockdown with HDR/NHEJ reporters, and post-damage RNase P activity assays

    PMID:28432356

    Open questions at the time
    • Mechanism by which Rpp29 promotes HDR at the break is undefined
    • Whether the catalytic RNase P activity itself acts at breaks unresolved
  10. 2016 Medium

    Identified Rpp29 as a chromatin factor that represses H3.3 nucleosome deposition at transcriptionally active loci.

    Evidence Live-cell imaging of tagged H3.3 at an inducible transgene array with siRNA knockdown and co-localization

    PMID:26842893

    Open questions at the time
    • Direct H3.3-binding interface not yet defined
    • Mechanism of deposition repression unclear
  11. 2018 Medium

    Mapped a direct, eukaryote-specific Rpp29-H3.3 interaction to its N-terminal extension and connected Rpp29 to histone PTM landscapes and oncogenic H3.3 mutations.

    Evidence Co-IP/pull-down with N-terminal truncations, Rpp29 knockdown in H3.3 G34V glioma cells, ChIP for histone PTMs, and RNA expression analysis

    PMID:29921582

    Open questions at the time
    • Functional consequence of the G34V-altered interaction not mechanistically resolved
    • Relationship between chromatin role and RNase P catalytic role unclear
    • Single lab

Open questions

Synthesis pass · forward-looking unresolved questions
  • How Rpp29 partitions among its three roles — RNase P catalysis, PARP1-dependent DNA repair, and H3.3 chromatin regulation — and whether these activities are coordinated remains unresolved.
  • No structure of the human heterodimer on human RNase P RNA
  • Mechanism linking PAR-binding recruitment to HDR not defined
  • Whether catalytic RNase P activity contributes to chromatin/repair functions unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0042393 histone binding 2 GO:0060090 molecular adaptor activity 2 GO:0140098 catalytic activity, acting on RNA 2
Localization
GO:0000228 nuclear chromosome 3 GO:0005634 nucleus 3
Pathway
R-HSA-4839726 Chromatin organization 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-73894 DNA Repair 1
Partners
H2BH3.3PARP1RPP21
Complex memberships
RNase PRpp21-Rpp29 heterodimer

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 Rpp29 (POP4) is a protein subunit of human RNase P; polyclonal antibodies against recombinant Rpp29 precipitate catalytically active RNase P from HeLa cells, establishing its presence in the active holoenzyme. cDNA cloning, immunoprecipitation of catalytically active RNase P with polyclonal antibodies against recombinant Rpp29 RNA (New York, N.Y.) Medium 10024167
2003 The archaeal Rpp29 homolog (Mth11/Mth Rpp29) adopts an oligonucleotide/oligosaccharide binding (OB) fold with a structured beta-barrel core and flexible N- and C-terminal extensions; it is an essential protein component of the archaeal RNase P holoenzyme as shown by reconstitution, and contacts the RNase P RNA subunit as identified by NMR chemical shift perturbation. Solution NMR structure determination, reconstitution experiments with recombinant subunits, NMR chemical shift perturbation for protein-RNA interaction mapping Proceedings of the National Academy of Sciences of the United States of America High 14673079
2003 The Archaeoglobus fulgidus Rpp29 homolog (an archaeal homolog of human Rpp29/yeast Pop4) forms a six-stranded antiparallel beta-sheet with flexible N- and C-terminal tails; conserved surface residues in the beta2-beta3 and beta4-beta5 loops and in the terminal tails are likely sites for RNA and protein interactions within RNase P. Multidimensional NMR structure determination, amide proton exchange, 15N relaxation rate measurements Biochemistry High 14622001
2004 The crystal structure of archaeal Rpp29 homolog Ph1771p reveals an OB-fold beta-barrel with topological similarity to RNA-binding proteins Hfq and L21E; two potential RNA-binding sites are identified: a concave surface with clustered positive charges (helices alpha1-alpha4 and strand beta6) and a loop (beta2-beta3) with conserved hydrophilic residues interacting with sulfate ion. X-ray crystallography at 2.0 Å resolution, structural comparison RNA (New York, N.Y.) High 15317976
2008 Human Rpp21 and Rpp29 bind each other, and together with catalytic H1 RNA are sufficient to activate endonucleolytic cleavage of precursor tRNA; the crystal structure of the archaeal PhoRpp21-PhoRpp29 heterodimer reveals that PhoRpp21's N-terminal helices (alpha1, alpha2) interact with PhoRpp29's N-terminal extended structure, beta-strand beta2, and C-terminal helix alpha3 via hydrogen bonds and salt bridges, forming a positively charged RNA-binding surface. Crystal structure determination of PhoRpp21-PhoRpp29 complex, mutational analysis, in vitro reconstitution of endonucleolytic cleavage activity Journal of molecular biology High 18929577
2008 The solution structure of Pyrococcus furiosus RPP21 and NMR chemical shift perturbations show that its two alpha-helices form the primary contact surface with RPP29, establishing the structural basis of RPP21-RPP29 interaction within the archaeal RNase P holoenzyme. Solution NMR structure determination, paramagnetic NMR, chemical shift perturbation analysis Biochemistry High 18922021
2009 The solution NMR structure of the P. furiosus RPP21-RPP29 complex reveals a 30-kDa heterodimer formed by coupled folding of secondary structural elements at the interface; enzymatic footprinting localizes the RPP21-RPP29 complex to the specificity (S) domain of the RNase P RNA, and conserved basic surface residues are identified as likely contacts for RPR and/or pre-tRNA. Solution NMR structure of protein-protein complex, enzymatic footprinting, chemical shift perturbation Journal of molecular biology High 19733182
2010 Using chimeric RNase P RNAs composed of swapped C- and S-domains from E. coli M1 RNA and P. horikoshii PhopRNA, PhoRpp21 and PhoRpp29 (archaeal homologs of human Rpp21 and Rpp29) are shown to function in stabilization/activation of the PhopRNA S-domain (specificity domain), while PhoPop5 and PhoRpp30 function on the C-domain. Chimeric RNA construction, in vitro RNase P activity assays with purified protein subunits Bioscience, biotechnology, and biochemistry Medium 20139629
2012 Isothermal titration calorimetry of P. furiosus RPP21-RPP29 interaction reveals binding-coupled protein folding as a major thermodynamic contributor to complex formation (large negative heat capacity change), with a strong salt dependence and proton release at neutral pH; a folding-deficient RPP21 point mutant confirms that coupled folding drives the excess heat capacity change. Isothermal titration calorimetry (ITC), NMR spectroscopy, site-directed mutagenesis of RPP21 Biochemistry High 22243443
2016 Rpp29 (along with Rpp21) is recruited to laser-microirradiated DNA damage sites in a PARP1-dependent manner by binding poly ADP-ribose moieties; depletion of Rpp29 and Rpp21 impairs homology-directed repair (HDR) of double-strand breaks but does not affect non-homologous end joining; additionally, depletion of the H1 RNA catalytic subunit diminishes their recruitment to damage sites, and RNase P activity is augmented after DNA damage in a PARP1-dependent manner. Laser microirradiation with live-cell imaging, siRNA knockdown, HDR and NHEJ reporter assays, poly ADP-ribose binding assays, RNase P activity assays after DNA damage Scientific reports High 28432356
2016 Rpp29 is a component of an H3.3/RNA complex at transcriptionally active genomic loci; Rpp29 knockdown increases H3.3 chromatin incorporation at a reporter array, establishing Rpp29 as a repressor of H3.3 nucleosome deposition. Fluorescence live-cell imaging of tagged H3.3 at inducible transgene array, siRNA knockdown, co-localization analysis Molecular biology of the cell Medium 26842893
2018 Rpp29 directly interacts with histone H3.3 through a sequence element in its own N-terminus, and also interacts with histone H2B at an adjacent site (the N-terminal region is absent in archaeal Rpp29, suggesting eukaryote-specific evolution); Rpp29 represses H3.3 incorporation into transcriptionally active genes, represses mRNA/protein expression and antisense RNA, and promotes heterochromatic PTMs (H3K9me3, H3K27me3) while repressing euchromatic PTMs; oncogenic H3.3 mutations (G34V) alter the H3.3-Rpp29 interaction. Biochemical interaction assay (pull-down/co-IP with N-terminal truncations), Rpp29 knockdown in KNS42 (H3.3 G34V) glioma cells, ChIP for histone PTMs, RNA expression analysis The Journal of biological chemistry Medium 29921582
2016 Mutational analysis of PhoRpp21-PhoRpp29 complex shows that PhoRpp21 binds the P11-P12 loop in the PhopRNA S-domain via overall positive surface charges, while Lys53, Lys54, Lys56 in PhoRpp21's alpha2 helix and the 10 C-terminal residues of PhoRpp29 are essential for PhopRNA activation; PhoRpp29 alone has reduced affinity for PhopRNA compared to PhoRpp21, indicating PhoRpp21 is the primary RNA-binding element in the heterodimer. Pull-down assay for protein-RNA binding, site-directed mutagenesis of PhoRpp21 and PhoRpp29, in vitro RNase P activity assays with deletion mutants of PhopRNA Biochemical and biophysical research communications Medium 27810361

Source papers

Stage 0 corpus · 15 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 Rpp14 and Rpp29, two protein subunits of human ribonuclease P. RNA (New York, N.Y.) 48 10024167
2003 Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P. Proceedings of the National Academy of Sciences of the United States of America 40 14673079
2009 Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions. Journal of molecular biology 34 19733182
2008 Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P. Journal of molecular biology 34 18929577
2004 Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29. RNA (New York, N.Y.) 32 15317976
2017 A role of human RNase P subunits, Rpp29 and Rpp21, in homology directed-repair of double-strand breaks. Scientific reports 26 28432356
2003 NMR structure of an archaeal homologue of ribonuclease P protein Rpp29. Biochemistry 26 14622001
2016 RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition. Molecular biology of the cell 24 26842893
2008 Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner. Biochemistry 19 18922021
2010 Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 work on distinct functional domains of the RNA subunit. Bioscience, biotechnology, and biochemistry 18 20139629
2018 Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. The Journal of biological chemistry 16 29921582
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
2012 Thermodynamics of coupled folding in the interaction of archaeal RNase P proteins RPP21 and RPP29. Biochemistry 9 22243443
2003 Preparation of uniformly labeled NMR samples in Escherichia coli under the tight control of the araBAD promoter: expression of an archaeal homolog of the RNase P Rpp29 protein. Protein expression and purification 8 12699688
2016 Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis. Biochemical and biophysical research communications 2 27810361

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