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7  structures 7552  species 0  interactions 8851  sequences 36  architectures

Family: YbeY (PF02130)

Summary: Endoribonuclease YbeY

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Endoribonuclease YbeY Provide feedback

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 [2,3,4]. 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 [5].

Literature references

  1. Penhoat CH, Li Z, Atreya HS, Kim S, Yee A, Xiao R, Murray D, Arrowsmith CH, Szyperski T; , J Struct Funct Genomics. 2005;6:51-62.: NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure. PUBMED:15965736 EPMC:15965736

  2. Jacob AI, Kohrer C, Davies BW, RajBhandary UL, Walker GC;, Mol Cell. 2013;49:427-438.: Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. PUBMED:23273979 EPMC:23273979

  3. Davies BW, Kohrer C, Jacob AI, Simmons LA, Zhu J, Aleman LM, Rajbhandary UL, Walker GC;, Mol Microbiol. 2010;78:506-518.: Role of Escherichia coli YbeY, a highly conserved protein, in rRNA processing. PUBMED:20807199 EPMC:20807199

  4. Xia Y, Weng Y, Xu C, Wang D, Pan X, Tian Z, Xia B, Li H, Chen R, Liu C, Jin Y, Bai F, Cheng Z, Kuipers OP, Wu W;, mBio. 2020; [Epub ahead of print]: Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa. PUBMED:32605982 EPMC:32605982

  5. Oganesyan V, Busso D, Brandsen J, Chen S, Jancarik J, Kim R, Kim SH;, Acta Crystallogr D Biol Crystallogr. 2003;59:1219-1223.: Structure of the hypothetical protein AQ_1354 from Aquifex aeolicus. PUBMED:12832766 EPMC:12832766


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002036

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 matured 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 [ PUBMED:20639334 , PUBMED:20807199 , PUBMED:23273979 , PUBMED:16511207 , PUBMED:32605982 ].

The crystal structure of the protein from the hyperthermophilic bacteria Aquifex aeolicus has been determined. The overall fold consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis reveals a good resemblance to the metal-dependent proteinases such as collagenases and gelatinases. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions [ PUBMED:12832766 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(208)
Full
(8851)
Representative proteomes UniProt
(42306)
RP15
(1296)
RP35
(4414)
RP55
(9015)
RP75
(15183)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(208)
Full
(8851)
Representative proteomes UniProt
(42306)
RP15
(1296)
RP35
(4414)
RP55
(9015)
RP75
(15183)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(208)
Full
(8851)
Representative proteomes UniProt
(42306)
RP15
(1296)
RP35
(4414)
RP55
(9015)
RP75
(15183)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: IPR002036
Previous IDs: UPF0054;
Type: Family
Sequence Ontology: SO:0100021
Author: Mian N , Bateman A
Number in seed: 208
Number in full: 8851
Average length of the domain: 134.9 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 75.32 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.0 25.9
Noise cut-off 24.7 24.6
Model length: 131
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the YbeY domain has been found. There are 7 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0H3GPX7 View 3D Structure Click here
A0A0P0V805 View 3D Structure Click here
A0A0R0GDI7 View 3D Structure Click here
A0A1D6H6J6 View 3D Structure Click here
A0A1D6ND07 View 3D Structure Click here
A0A2R8QTM9 View 3D Structure Click here
A0JX41 View 3D Structure Click here
A0KN83 View 3D Structure Click here
A0L7K6 View 3D Structure Click here
A0LK95 View 3D Structure Click here
A0LT03 View 3D Structure Click here
A0Q1Q3 View 3D Structure Click here
A0R0T0 View 3D Structure Click here
A1A1B9 View 3D Structure Click here
A1AVF9 View 3D Structure Click here
A1B8B6 View 3D Structure Click here
A1BH76 View 3D Structure Click here
A1K3J2 View 3D Structure Click here
A1R6V9 View 3D Structure Click here
A1S8S3 View 3D Structure Click here
A1SHY8 View 3D Structure Click here
A1SSC2 View 3D Structure Click here
A1TBR2 View 3D Structure Click here
A1TUZ4 View 3D Structure Click here
A1UIQ4 View 3D Structure Click here
A1UU41 View 3D Structure Click here
A1VJK1 View 3D Structure Click here
A1WC38 View 3D Structure Click here
A1WQ64 View 3D Structure Click here
A1WVF5 View 3D Structure Click here
A2SKV4 View 3D Structure Click here
A3CP96 View 3D Structure Click here
A3DEC2 View 3D Structure Click here
A3N058 View 3D Structure Click here
A3PAQ0 View 3D Structure Click here
A3QH43 View 3D Structure Click here
A4F9T1 View 3D Structure Click here
A4G265 View 3D Structure Click here
A4IA97 View 3D Structure Click here
A4J7D9 View 3D Structure Click here