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283  structures 8825  species 0  interactions 41149  sequences 353  architectures

Family: tRNA-synt_2b (PF00587)

Summary: tRNA synthetase class II core domain (G, H, P, S and T)

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

tRNA synthetase class II core domain (G, H, P, S and T) Provide feedback

tRNA-synt_2b is a family of largely threonyl-tRNA members.

Literature references

  1. Cusack S; , Nat Struct Biol 1995;2:824-831.: Eleven down and nine to go. PUBMED:7552701 EPMC:7552701

  2. 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


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002314

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 ].

This domain is the core catalytic domain of tRNA synthetases and includes glycyl, prolyl, seryl and threonyl tRNA synthetases.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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_synt_II (CL0040), which has the following description:

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).

The clan contains the following 11 members:

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 tRNA_synthFbeta

Alignments

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 and the UniProtKB sequence database. More...

View options

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
(8)
Full
(41149)
Representative proteomes UniProt
(169454)
RP15
(6408)
RP35
(20079)
RP55
(39379)
RP75
(63415)
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HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(8)
Full
(41149)
Representative proteomes UniProt
(169454)
RP15
(6408)
RP35
(20079)
RP55
(39379)
RP75
(63415)
Alignment:
Format:
Order:
Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(8)
Full
(41149)
Representative proteomes UniProt
(169454)
RP15
(6408)
RP35
(20079)
RP55
(39379)
RP75
(63415)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: pdb_id 3ial,2dq3,3ugt,1evk,3vbb,1kmn,2j3l,3a31
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 8
Number in full: 41149
Average length of the domain: 220.60 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 39.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 29.3 29.3
Trusted cut-off 29.3 29.3
Noise cut-off 29.2 29.2
Model length: 179
Family (HMM) version: 27
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 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 tRNA-synt_2b domain has been found. There are 283 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2JZI2 View 3D Structure Click here
A0A0R4ISX2 View 3D Structure Click here
A0A143ZZQ0 View 3D Structure Click here
A0A144A0G8 View 3D Structure Click here
A0A1D6E223 View 3D Structure Click here
A0A1D6EC22 View 3D Structure Click here
A0A1D6GKX7 View 3D Structure Click here
A0A1D6HSW9 View 3D Structure Click here
A0A1D6II54 View 3D Structure Click here
A0A1D6KKI8 View 3D Structure Click here
A0A1D6KSQ7 View 3D Structure Click here
A0A1D6PQL3 View 3D Structure Click here
A0A1D8PCV0 View 3D Structure Click here
A0A1D8PMV9 View 3D Structure Click here
A0A1D8PRZ3 View 3D Structure Click here
A2BIM7 View 3D Structure Click here
A2RTX5 View 3D Structure Click here
A3QJX4 View 3D Structure Click here
A4HUS2 View 3D Structure Click here
A4HXZ5 View 3D Structure Click here
A4HY00 View 3D Structure Click here
A4IB34 View 3D Structure Click here
B4FQC4 View 3D Structure Click here
B4FRC4 View 3D Structure Click here
C0PGQ1 View 3D Structure Click here
D3ZM09 View 3D Structure Click here
F1Q6U0 View 3D Structure Click here
F1QHZ4 View 3D Structure Click here
F1QP23 View 3D Structure Click here
F1QUV7 View 3D Structure Click here
F4IFC5 View 3D Structure Click here
G5EF77 View 3D Structure Click here
I1J5B4 View 3D Structure Click here
I1JC08 View 3D Structure Click here
I1JQX3 View 3D Structure Click here
I1JVB5 View 3D Structure Click here
I1KZJ9 View 3D Structure Click here
I1L332 View 3D Structure Click here
I1LBD0 View 3D Structure Click here
I1MPJ4 View 3D Structure Click here
I1NAJ0 View 3D Structure Click here
I1NBI4 View 3D Structure Click here
I1NIY6 View 3D Structure Click here
K7KUA0 View 3D Structure Click here
K7LYN7 View 3D Structure Click here
K7UDG5 View 3D Structure Click here
O04630 View 3D Structure Click here
O13969 View 3D Structure Click here
O14018 View 3D Structure Click here
O23627 View 3D Structure Click here
O45869 View 3D Structure Click here
O60155 View 3D Structure Click here
O74765 View 3D Structure Click here
P04801 View 3D Structure Click here
P07236 View 3D Structure Click here
P07284 View 3D Structure Click here
P07814 View 3D Structure Click here
P0A8L1 View 3D Structure Click here
P0A8M3 View 3D Structure Click here
P16659 View 3D Structure Click here
P26638 View 3D Structure Click here
P26639 View 3D Structure Click here
P28668 View 3D Structure Click here
P38705 View 3D Structure Click here
P38708 View 3D Structure Click here
P39965 View 3D Structure Click here
P41250 View 3D Structure Click here
P49591 View 3D Structure Click here
P52709 View 3D Structure Click here
P60906 View 3D Structure Click here
P87144 View 3D Structure Click here
P95689 View 3D Structure Click here
P9WFT5 View 3D Structure Click here
P9WFT7 View 3D Structure Click here
P9WFT9 View 3D Structure Click here
P9WFV7 View 3D Structure Click here
Q06817 View 3D Structure Click here
Q0D8E4 View 3D Structure Click here
Q10039 View 3D Structure Click here
Q10QF5 View 3D Structure Click here
Q18678 View 3D Structure Click here
Q22620 View 3D Structure Click here
Q2FXP7 View 3D Structure Click here
Q2FY08 View 3D Structure Click here
Q2G1Z4 View 3D Structure Click here
Q2QS11 View 3D Structure Click here
Q2R1C1 View 3D Structure Click here
Q39230 View 3D Structure Click here
Q3UQ84 View 3D Structure Click here
Q4CW46 View 3D Structure Click here
Q4D9G6 View 3D Structure Click here
Q4DC68 View 3D Structure Click here
Q4DLK5 View 3D Structure Click here
Q4DPR0 View 3D Structure Click here
Q4DZZ4 View 3D Structure Click here
Q54J66 View 3D Structure Click here
Q54PF9 View 3D Structure Click here
Q54Q07 View 3D Structure Click here
Q55GM6 View 3D Structure Click here
Q57681 View 3D Structure Click here
Q58477 View 3D Structure Click here
Q58597 View 3D Structure Click here
Q58635 View 3D Structure Click here
Q59R20 View 3D Structure Click here
Q59RK3 View 3D Structure Click here
Q5A2A5 View 3D Structure Click here
Q5I0G4 View 3D Structure Click here
Q5JKQ3 View 3D Structure Click here
Q5M7W7 View 3D Structure Click here
Q5XHY5 View 3D Structure Click here
Q5XI17 View 3D Structure Click here
Q68FW7 View 3D Structure Click here
Q6DRC0 View 3D Structure Click here
Q6ER90 View 3D Structure Click here
Q6P799 View 3D Structure Click here
Q6Z0N5 View 3D Structure Click here
Q6ZD35 View 3D Structure Click here
Q75JK9 View 3D Structure Click here
Q7KWQ2 View 3D Structure Click here
Q7L3T8 View 3D Structure Click here
Q8BLY2 View 3D Structure Click here
Q8CFI5 View 3D Structure Click here
Q8CGC7 View 3D Structure Click here
Q8GZ45 View 3D Structure Click here
Q8I2Q5 View 3D Structure Click here
Q8IBS3 View 3D Structure Click here
Q8IIA4 View 3D Structure Click here
Q8MP20 View 3D Structure Click here
Q8RWT8 View 3D Structure Click here
Q9BW92 View 3D Structure Click here
Q9CZD3 View 3D Structure Click here
Q9D0R2 View 3D Structure Click here
Q9FXG2 View 3D Structure Click here
Q9FYR6 View 3D Structure Click here
Q9HGT6 View 3D Structure Click here
Q9JJL8 View 3D Structure Click here
Q9M1R2 View 3D Structure Click here
Q9NP81 View 3D Structure Click here
Q9UTB2 View 3D Structure Click here
Q9VF85 View 3D Structure Click here
Q9VKB0 View 3D Structure Click here
Q9VQL1 View 3D Structure Click here
Q9VUK8 View 3D Structure Click here
Q9VZY9 View 3D Structure Click here