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729  structures 5420  species 47  interactions 76350  sequences 627  architectures

Clan: tRNA_synt_II (CL0040)


Class II aminoacyl-tRNA and Biotin synthetases Add an annotation

Aminoacyl-tRNA synthetases are key components of the protein translation machinery that catalyse two basic reactions. First, the activation of amino acids via the formation of aminoacyl adenylates and second, linking the activated amino acid to the cognate tRNAs. The aminoacyl-tRNA synthetases generate AMP as the second end product of this reaction, which differentiates them from the majority of ATP-dependent enzymes that produce ADP. In addition, there is a specific aminoacyl-tRNA synthetases for each of the 20 amino acids and there are two structurally distinct classes of aminoacyl-tRNA synthetases, each encompassing 10 different specificities. The two classes have alternative modes of aminoacylation: class I aminoacylate the 2'OH of the cognate tRNA; class II aminoacylate 3'OH (with the exception of PheRS). Each class contain a conserved core domain that is involved in ATP binding and hydrolysis and combines with additional domains that determine the specificity of interactions with the cognate amino acid and tRNA. The class II core domain consist of a mixed-beta sheet, similar to that found in the biotin synthetases, hence why this family has also been included in this clan. The core domain contains three modestly conserved motifs that are responsible for ATP binding. The class II aminoacyl-tRNA synthetases can contain additional nested domains, found inserted in the loops of the core domain [1] (and reference therein).

This clan contains 10 families and the total number of domains in the clan is 76350. The clan was built by RD Finn.

Literature references

  1. Wolf YI, Aravind L, Grishin NV, Koonin EV; , Genome Res 1999;9:689-710.: Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. PUBMED:10447505 EPMC:10447505


This clan contains the following 10 member families:

AsnA BPL_LplA_LipB BPL_LplA_LipB_2 DUF366 tRNA-synt_2 tRNA-synt_2b tRNA-synt_2c tRNA-synt_2d tRNA-synt_2e tRNA-synt_His

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

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The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
tRNA-synt_2b (PF00587) 21534 (28.2%) View
tRNA-synt_2 (PF00152) 17822 (23.3%) View
BPL_LplA_LipB (PF03099) 10146 (13.3%) View
tRNA-synt_His (PF13393) 8752 (11.5%) View
tRNA-synt_2c (PF01411) 7576 (9.9%) View
tRNA-synt_2d (PF01409) 7096 (9.3%) View
tRNA-synt_2e (PF02091) 2339 (3.1%) View
AsnA (PF03590) 840 (1.1%) View
BPL_LplA_LipB_2 (PF16917) 156 (0.2%) View
DUF366 (PF04017) 89 (0.1%) View
Total: 10 Total: 76350 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

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