Summary: Aminoacyl tRNA synthetase class II, N-terminal domain
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Aminoacyl tRNA synthetase class II, N-terminal domain Provide feedback
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Literature references
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Mosyak L, Reshetnikova L, Goldgur Y, Delarue M, Safro MG; , Nat Struct Biol 1995;2:537-547.: Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus. PUBMED:7664121 EPMC:7664121
External database links
SCOP: | 1eiy |
This tab holds annotation information from the InterPro database.
InterPro entry IPR004188
Phenylalanine-tRNA ligase (also known as phenylalanyl-tRNA synthetase) from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the ligase family. Identification of phenylalanine-tRNA ligase a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other ligases [PUBMED:8199244]. This is the N-terminal domain of phenylalanine-tRNA ligase.
The aminoacyl-tRNA synthetases (also known as aminoacyl-tRNA ligases) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [PUBMED:10704480,PUBMED:12458790]. These proteins differ widely in size and oligomeric state, and have limited sequence homology [PUBMED:2203971]. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric [PUBMED:10673435]. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [PUBMED:8364025], and are mostly dimeric or multimeric, containing at least three conserved regions [PUBMED:8274143, PUBMED:2053131, PUBMED:1852601]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan, valine, and some lysine synthetases (non-eukaryotic group) belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, phenylalanine, proline, serine, threonine, and some lysine synthetases (non-archaeal group), belong to class-II synthetases. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c [PUBMED:10447505].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cytoplasm (GO:0005737) |
Molecular function | phenylalanine-tRNA ligase activity (GO:0004826) |
ATP binding (GO:0005524) | |
nucleotide binding (GO:0000166) | |
Biological process | phenylalanyl-tRNA aminoacylation (GO:0006432) |
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 tRNA_bind_arm (CL0298), which has the following description:
This domain is found in Phe and Ser tRNA synthetases at the N-terminus, and at the C-terminus of Val tRNA synthetase. The domain is composed of two helices.
The clan contains the following 3 members:
Phe_tRNA-synt_N Seryl_tRNA_N Val_tRNA-synt_CAlignments
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 (765) |
Full (6520) |
Representative proteomes | UniProt (31355) |
NCBI (35161) |
Meta (1973) |
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RP15 (857) |
RP35 (3172) |
RP55 (6593) |
RP75 (11469) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (765) |
Full (6520) |
Representative proteomes | UniProt (31355) |
NCBI (35161) |
Meta (1973) |
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RP15 (857) |
RP35 (3172) |
RP55 (6593) |
RP75 (11469) |
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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: | Structural domain |
Previous IDs: | tRNA-synt_2_N; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Griffiths-Jones SR |
Number in seed: | 765 |
Number in full: | 6520 |
Average length of the domain: | 68.80 aa |
Average identity of full alignment: | 31 % |
Average coverage of the sequence by the domain: | 19.88 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 69 | ||||||||||||
Family (HMM) version: | 19 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
tRNA-synt_2dStructures
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 Phe_tRNA-synt_N domain has been found. There are 12 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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