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240  structures 7796  species 0  interactions 29089  sequences 213  architectures

Family: Ribonuc_L-PSP (PF01042)

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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

External database links

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 14.5kDa 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_endoribonc


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.

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Representative proteomes UniProt

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

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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...


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: Pfam-B_797 (release 3.0)
Previous IDs: DUF10;UPF0076; ribonuc_L-PSP;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Finn RD , Kerrison ND
Number in seed: 25
Number in full: 29089
Average length of the domain: 117 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 71.01 %

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 27.3 27.3
Trusted cut-off 27.3 27.3
Noise cut-off 27.2 27.2
Model length: 121
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 240 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
A0A077Z8Z3 View 3D Structure Click here
A0A0D2D985 View 3D Structure Click here
A0A0D2DAJ1 View 3D Structure Click here
A0A0D2DUS0 View 3D Structure Click here
A0A0D2E4Z5 View 3D Structure Click here
A0A0D2E600 View 3D Structure Click here
A0A0D2EIE3 View 3D Structure Click here
A0A0D2F1G9 View 3D Structure Click here
A0A0D2GAZ0 View 3D Structure Click here
A0A0D2GRZ8 View 3D Structure Click here
A0A0D2GS03 View 3D Structure Click here
A0A0D2GZQ6 View 3D Structure Click here
A0A0H3GHF4 View 3D Structure Click here
A0A0H3GHI2 View 3D Structure Click here
A0A0H3GL84 View 3D Structure Click here
A0A0H3GMT0 View 3D Structure Click here
A0A0H3GQX3 View 3D Structure Click here
A0A0H3GS95 View 3D Structure Click here
A0A0H3GUP5 View 3D Structure Click here
A0A0H3GZG2 View 3D Structure Click here
A0A0K0DT50 View 3D Structure Click here
A0A158Q437 View 3D Structure Click here
A0A175VRU0 View 3D Structure Click here
A0A175W0N7 View 3D Structure Click here
A0A175W271 View 3D Structure Click here
A0A175W2I4 View 3D Structure Click here
A0A175W9E9 View 3D Structure Click here
A0A175WEF5 View 3D Structure Click here
A0A1C1CCG3 View 3D Structure Click here
A0A1C1CG90 View 3D Structure Click here
A0A1C1CIH1 View 3D Structure Click here
A0A1C1CRS7 View 3D Structure Click here
A0A1C1CSK3 View 3D Structure Click here
A0A1C1D036 View 3D Structure Click here
A0A1C1D123 View 3D Structure Click here
A0A1D6HNY1 View 3D Structure Click here
A0A1D8PDX5 View 3D Structure Click here
A0A1D8PGY1 View 3D Structure Click here
A4VQH6 View 3D Structure Click here
A6T7A0 View 3D Structure Click here