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 . Previously thought to inhibit protein synthesis initiation . This protein may also be involved in the regulation of purine biosynthesis . YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase . YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella .
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
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
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
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
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
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR006175
The YjgF/YER057c/UK114 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].
This family includes:
- YjgF (RidA), which contains the 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]
- Rhp-PSP from Rhodopseudomonas palustris strain JSC-3b, which has antiviral properties [PUBMED:26530252].
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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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Curation and family details
|Seed source:||Pfam-B_797 (release 3.0)|
|Previous IDs:||DUF10;UPF0076; ribonuc_L-PSP;|
|Author:||Bateman A, Finn RD, Kerrison ND|
|Number in seed:||29|
|Number in full:||7806|
|Average length of the domain:||116.60 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||68.46 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||19|
|Download:||download the raw HMM for this family|
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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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