Summary: Endoribonuclease L-PSP
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Endoribonuclease L-PSP Provide feedback
Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA [1]. Previously thought to inhibit protein synthesis initiation [2]. This protein may also be involved in the regulation of purine biosynthesis [3]. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase [5]. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella [4].
Literature references
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Morishita R, Kawagoshi A, Sawasaki T, Madin K, Ogasawara T, Oka T, Endo Y; , J Biol Chem 1999;274:20688-20692.: Ribonuclease activity of rat liver perchloric acid-soluble protein, a potent inhibitor of protein synthesis. PUBMED:10400702 EPMC:10400702
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Oka T, Tsuji H, Noda C, Sakai K, Hong YM, Suzuki I, Munoz S, Natori Y; , J Biol Chem 1995;270:30060-30067.: Isolation and characterization of a novel perchloric acid-soluble protein inhibiting cell-free protein synthesis. PUBMED:8530410 EPMC:8530410
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Rappu P, Shin BS, Zalkin H, Mantsala P; , J Bacteriol 1999;181:3810-3815.: A role for a highly conserved protein of unknown function in regulation of Bacillus subtilis purA by the purine repressor. PUBMED:10368157 EPMC:10368157
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Schmitz G, Downs DM;, J Bacteriol. 2004;186:803-810.: Reduced transaminase B (IlvE) activity caused by the lack of yjgF is dependent on the status of threonine deaminase (IlvA) in Salmonella enterica serovar Typhimurium. PUBMED:14729707 EPMC:14729707
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Lambrecht JA, Flynn JM, Downs DM;, J Biol Chem. 2012;287:3454-3461.: Conserved YjgF Protein Family Deaminates Reactive Enamine/Imine Intermediates of Pyridoxal 5'-Phosphate (PLP)-dependent Enzyme Reactions. PUBMED:22094463 EPMC:22094463
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Thakur KG, Praveena T, Gopal B;, Proteins. 2010;78:773-778.: Mycobacterium tuberculosis Rv2704 is a member of the YjgF/YER057c/UK114 family. PUBMED:19899170 EPMC:19899170
Internal database links
SCOOP: | Rab3-GTPase_cat YjgF_endoribonc |
Similarity to PfamA using HHSearch: | YjgF_endoribonc |
External database links
HOMSTRAD: | UPF0076 |
PROSITE: | PDOC00838 |
SCOP: | 1qd9 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006175
The YjgF/YER057c/UK114 family (also known as the Rid family) of proteins is conserved in all domains of life [PUBMED:22094463]. A phylogenetic analysis applied by Lambrecht et al. has divided the Rid family into a widely distributed archetypal RidA (YjgF) subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other [PUBMED:25975565]. Although the family members share high levels of protein sequence and structue similarity, their functions vary widely across different species [PUBMED:4632080].
Structurally, these proteins are homotrimers with clefts between the monomeric subunits that are proposed to have some functional relevance [PUBMED:19899170, PUBMED:12112709, PUBMED:10595546].
This family includes:
- YjgF (also known as RidA or 2-iminobutanoate/2-iminopropanoate deaminase), which displays enamine/imine deaminase activity and can accelerate the release of ammonia from reactive enamine/imine intermediates of the pyridoxal 5'-phosphate-dependent threonine dehydratase (IlvA) [PUBMED:22094463, PUBMED:18296521]
- the yeast growth inhibitor YER057c (protein HMF1) that appears to play a role in the regulation of metabolic pathways and cell differentiation [PUBMED:11442631]
- the mammalian 14.5 kDa translational inhibitor protein UK114, also known as L-PSP (liver perchloric acid-soluble protein), with endoribonucleolytic activity that directly affects mRNA translation and can induce disaggregation of the reticulocyte polysomes into 80 S ribosomes [PUBMED:10400702]
- RutC from E. coli, which is essential for growth on uracil as sole nitrogen source and is thought to reduce aminoacrylate peracid to aminoacrylate [PUBMED:20400551]
- YabJ from B. subtilis, which is required for adenine-mediated repression of purine biosynthetic genes [PUBMED:10557275]
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan YjgF-like (CL0534), which has the following description:
This superfamily is characterised by proteins that form trimers with three closely packed beta-sheets. Some member proteins are chorismate mutases, others are endoribonucleases active on single-stranded mRNA. It is the highly conserved YjgF/YER057c/UK114 protein superfamily. Homologues of this protein occur in eubacteria, archaea, and eukaryotes. Proteins are functionally diverse and are involved in a variety of enzymatic and non-enzymatic functions. The high sequence and structural similarity between members of this protein superfamily offer an example of minimalistic changes leading to functional diversification. This feature is best exemplified by the three close homologues of YjgF proteins in mammals (human, rat, and goat) with sequence identity better than 85%. These homologues perform different functions, including tumour antigen activity in the goat homologue, translation inhibition in the human and rat homologues (hp14.5 and rp14.5), endoribonuclease activity in rp14.5, calpain activation in the bovine homologue, molecular chaperone activity in DUK114, and involvement in the regulation of purine and removal of toxic metabolites in YjgF7, and involvement in isoleucine biosynthetic pathways (YjgF, YER057c, Ibm1). In addition, members of this protein family have also been shown to regulate mitochondrial maintenance (Ibm1) in yeast. Proteins from the YjgF family in plants are involved in photosynthesis and chromoplastogenesis (CHRD).
The clan contains the following 4 members:
Amido_AtzD_TrzD CM_1 Ribonuc_L-PSP YjgF_endoriboncAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (29) |
Full (24388) |
Representative proteomes | UniProt (66515) |
NCBI (91700) |
Meta (3561) |
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RP15 (4616) |
RP35 (14093) |
RP55 (23405) |
RP75 (36007) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (29) |
Full (24388) |
Representative proteomes | UniProt (66515) |
NCBI (91700) |
Meta (3561) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (4616) |
RP35 (14093) |
RP55 (23405) |
RP75 (36007) |
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Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | Pfam-B_797 (release 3.0) |
Previous IDs: | DUF10;UPF0076; ribonuc_L-PSP; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 29 |
Number in full: | 24388 |
Average length of the domain: | 117.00 aa |
Average identity of full alignment: | 26 % |
Average coverage of the sequence by the domain: | 74.32 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 121 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
Ribonuc_L-PSPStructures
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 Ribonuc_L-PSP domain has been found. There are 180 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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