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175  structures 17588  species 1  interaction 46884  sequences 89  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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006175

The YjgF/Yer057p/UK114 family is a large, highly conserved, and widely distributed family of proteins found in bacteria, archaea and eukaryotes. YjgF (renamed RidA) deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions. The YjgF/YER057c/UK114 family of proteins is conserved in all domains of life suggesting that reactive enamine/imine metabolites are of concern to all organisms [PUBMED:22094463]. This family includes:

  • YjgF and its orthologues
  • the yeast growth inhibitor YER057cp 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]
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].

Domain organisation

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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 3 members:

CM_1 Ribonuc_L-PSP YjgF_endoribonc


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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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
Author: Bateman A, Finn RD, Kerrison ND
Number in seed: 29
Number in full: 46884
Average length of the domain: 116.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 86.15 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -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 27.1 27.2
Model length: 121
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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


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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 175 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 seqence.

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