Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
514  structures 5927  species 22  interactions 72316  sequences 340  architectures

Clan: tRNA_synt_II (CL0040)

Summary

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 9 families and the total number of domains in the clan is 72316. 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

Members

This clan contains the following 9 member families:

AsnA BPL_LplA_LipB DUF544 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...

Loading domain graphics...

Alignments

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) 18502 (25.6%) View
tRNA-synt_2 (PF00152) 16099 (22.3%) View
BPL_LplA_LipB (PF03099) 11826 (16.4%) View
tRNA-synt_His (PF13393) 7540 (10.4%) View
tRNA-synt_2c (PF01411) 6692 (9.3%) View
tRNA-synt_2d (PF01409) 6642 (9.2%) View
tRNA-synt_2e (PF02091) 3035 (4.2%) View
AsnA (PF03590) 1603 (2.2%) View
DUF544 (PF04424) 377 (0.5%) View
Total: 9 Total: 72316 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

Hide

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

Loading...

Interactions

There are 22 interactions for this clan. More...

Interacting families
A B
tRNA-synt_2b WHEP-TRS
tRNA-synt_2b
HisG
Seryl_tRNA_N
HGTP_anticodon
tRNA_edit
tRNA_SAD
ProRS-C_1
ProRS-C_2
AsnA AsnA
BPL_LplA_LipB BPL_C
BPL_LplA_LipB
HTH_11
Lip_prot_lig_C
tRNA-synt_2 tRNA-synt_2
tRNA_anti-codon
GAD
tRNA-synt_2c tRNA_SAD
tRNA-synt_2d tRNA-synt_2d
FDX-ACB
B3_4
B5

Structures

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.

Loading structure mapping...