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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

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Domain organisation

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Alignments

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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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  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.

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Curation and family details

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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: 134.90 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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