All families / PF02130
PF02130: YbeY
Endoribonuclease YbeY
- Curation status
- SEEDED
- Seed status
- EX DUF
- Characterization
- UNSCORED
Grounding
PF02130: Endoribonuclease YbeY
IPR002036: integrated entry for Endoribonuclease YbeY
Source description
YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs [InterPro reference PUB00064743,InterPro reference PUB00064742,InterPro reference PUB00096939]. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices [InterPro reference PUB00027806].
Evidence and references
- InterPro entry and its literature references. PUB identifiers are internal InterPro references, not PubMed identifiers. Unresolved citations link to the originating entry.
- Frozen description source: InterPro/Pfam API
Source descriptions and links are provenance, not independent functional validation.
Evidence counts: not scored.
Curated functional assertions
No curated functional assertions supplied.
Protein sequence examples
6 verified sequence examples. FASTA
| UniProt | Protein / organism | Sequence | Provenance |
|---|---|---|---|
| P0A898 | Endoribonuclease YbeY Escherichia coli (strain K12) | 155 aa; version 1 UniProt 2026_03 | PTM REGISTRY MIRROR16 sibling references
|
| P46347 | Endoribonuclease YbeY Bacillus subtilis (strain 168) | 157 aa; version 3 UniProt 2026_03 | UNIPROT FETCH |
| P58557 | Endoribonuclease YbeY Homo sapiens | 167 aa; version 2 UniProt 2026_03 | UNIPROT FETCH |
| Q62ML1 | Endoribonuclease YbeY Burkholderia mallei (strain ATCC 23344) | 184 aa; version 2 UniProt 2026_03 | UNIPROT FETCH1 sibling references |
| Q8CAV0 | Endoribonuclease YbeY Mus musculus | 164 aa; version 1 UniProt 2026_03 | UNIPROT FETCH |
| Q8L5Z4 | Endoribonuclease YBEY, chloroplastic Arabidopsis thaliana | 584 aa; version 1 UniProt 2026_03 | UNIPROT FETCH2 sibling references |
Pfam membership is not functional evidence. Whole-protein sequences do not establish domain boundaries. A coverage gap here is not absence from UniProt.
Sequences and metadata: UniProt Consortium, CC BY 4.0.
Domain matches
No residue-level domain match evidence is available in this build. Structure and AlphaFold counters do not supply coordinates or establish function.
Snapshot counters
- proteins
- 20,178
- matches
- 20,283
- proteomes
- 19,123
- taxa
- 29,306
- structures
- 5
- alphafold models
- 13,642
- domain architectures
- 53
Classification basis
pfam previous unknown name
No scoring reasons supplied.
Related Mech records
This family joined the worklist after the frozen cross-Mech scan, so other Mechs were not searched for it. Missing links here are not evidence that other Mechs lack it; rows shown come from mentions of a former DUF/UPF name.
No cross-Mech examples are present in the supplied snapshot.
Curation history and reviews
No retained curation events supplied.
No retained review supplied.
Record source
Status and evidence
- Seed status
- A name-based classification of frozen InterPro/Pfam metadata. UNKNOWN CANDIDATE means the metadata explicitly says the function is unknown. KNOWN HISTORICAL DUF means a DUF name matched without that wording; this heuristic is not proof of a known function and does not establish experimental characterization. EX DUF means Pfam renamed the family away from a DUF/UPF name, as recorded in Pfam's previous identifiers; a rename usually follows published work on some members but is naming history, not proof of function for every member. Some EX DUF families' current names or descriptions still say the function is unknown; their classification basis lists this, and scoring does not treat them as characterized. FALSE POSITIVE TEXT HIT means the naming rules did not match.
- Characterization
- A separate evidence-scoring result. UNSCORED means no score has been calculated; it is not evidence that the family lacks a known function. Missing scores are not negative evidence. PARTIALLY CHARACTERIZED has partial support; KNOWN HISTORICAL DUF can inherit the seed label or reflect a known-function signal. Neither label implies experimental validation.
- Evidence counts
- Source-specific signals, not unique proteins, publications, or confidence scores. Known counts Rhea reactions and experimentally supported GO molecular-function annotations. Partial counts functional/domain assignments. Context counts structural, environmental, orthology, interaction and neighborhood signals; context alone does not assign function. Repeated annotations may not be independent.
- Curation status
- Reported separately from seed classification and characterization. SNAPSHOT ONLY means no curated metadata was supplied for this build. SEEDED denotes a source-derived record, not an expert-reviewed functional claim.
- Missing counts
- Not available means the source did not supply that counter. A zero is a reported count. Not scored means evidence counts are unavailable.