Summary: YjgF/chorismate_mutase-like, putative endoribonuclease
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YjgF/chorismate_mutase-like, putative endoribonuclease Provide feedback
YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes [1].
Literature references
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Volz K;, Protein Sci. 1999;8:2428-2437.: A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli. PUBMED:10595546 EPMC:10595546
Internal database links
SCOOP: | Ribonuc_L-PSP |
Similarity to PfamA using HHSearch: | Ribonuc_L-PSP |
This tab holds annotation information from the InterPro database.
InterPro entry IPR013813
This entry represents the beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF/Yer057p/UK114 family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site [PUBMED:14624641, PUBMED:12777779, PUBMED:17506874, PUBMED:16323205].
Chorismate mutase (CM, EC) is an enzyme of the aromatic amino acid biosynthetic pathway that catalyses the reaction at the branch point of the pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. The structure of chorismate mutase enzymes from Bacillus subtilis [PUBMED:10818343] and Thermus thermophilus have been solved and were shown to have a catalytic homotrimer, with the active sites being located at the subunit interfaces, where residues from two subunits contribute to each site.
The YjgF/YER057c/UK114 family is a large, highly conserved, and widely distributed family of proteins found in bacteria, archaea and eukaryotes [PUBMED:22094463]. 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 (RidA) [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 (2) |
Full (4100) |
Representative proteomes | UniProt (10721) |
NCBI (13092) |
Meta (1483) |
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RP15 (796) |
RP35 (2546) |
RP55 (4162) |
RP75 (6129) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (2) |
Full (4100) |
Representative proteomes | UniProt (10721) |
NCBI (13092) |
Meta (1483) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (796) |
RP35 (2546) |
RP55 (4162) |
RP75 (6129) |
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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: | CATH:2otmA00 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Coggill P |
Number in seed: | 2 |
Number in full: | 4100 |
Average length of the domain: | 147.20 aa |
Average identity of full alignment: | 43 % |
Average coverage of the sequence by the domain: | 92.25 % |
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: | 148 | ||||||||||||
Family (HMM) version: | 6 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
YjgF_endoriboncStructures
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 YjgF_endoribonc domain has been found. There are 15 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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