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23  structures 8743  species 0  interactions 24424  sequences 148  architectures

Family: tRNA_SAD (PF07973)

Summary: Threonyl and Alanyl tRNA synthetase second additional domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

Threonyl and Alanyl tRNA synthetase second additional domain Provide feedback

The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain [1].

Literature references

  1. Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D; , Cell 1999;97:371-381.: The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. PUBMED:10319817 EPMC:10319817


This tab holds annotation information from the InterPro database.

InterPro entry IPR012947

The catalytically active form of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this SAD domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain [ PUBMED:10319817 ].

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 Peptidase_ME (CL0094), which has the following description:

All members of this clan are characterised by a HXXEH motif, which is is involved in zinc binding. Furthermore all members adopt an alpha and beta fold. More specifically, there us a four to six stranded antiparallel beta sheet surrounded by five helices. However, LuxS (PFAM:PF02664) is not a peptidase, although its hydrolytic mechanism of catalysis appears to be conserved [1].

The clan contains the following 7 members:

LuxS M16C_assoc Peptidase_M16 Peptidase_M16_C Peptidase_M16_M Peptidase_M44 tRNA_SAD

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
(196)
Full
(24424)
Representative proteomes UniProt
(105823)
RP15
(3678)
RP35
(11824)
RP55
(23518)
RP75
(38454)
Jalview View  View  View  View  View  View  View 
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
(196)
Full
(24424)
Representative proteomes UniProt
(105823)
RP15
(3678)
RP35
(11824)
RP55
(23518)
RP75
(38454)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(196)
Full
(24424)
Representative proteomes UniProt
(105823)
RP15
(3678)
RP35
(11824)
RP55
(23518)
RP75
(38454)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Pfam-B_270 (release 16.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 196
Number in full: 24424
Average length of the domain: 49.50 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 6.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 44
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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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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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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_SAD domain has been found. There are 23 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
A0A1D6GKX7 View 3D Structure Click here
A0A1D6II54 View 3D Structure Click here
A0A1D6JPE4 View 3D Structure Click here
A0A1D6KSQ7 View 3D Structure Click here
A0A1D6NR59 View 3D Structure Click here
A0A1D8PFC1 View 3D Structure Click here
A0A1D8PMV9 View 3D Structure Click here
A0A1I9LMV6 View 3D Structure Click here
A0A2R8QSU7 View 3D Structure Click here
A0A368UK73 View 3D Structure Click here
A2BIM7 View 3D Structure Click here
A2RTX5 View 3D Structure Click here
A4I013 View 3D Structure Click here
A4IB34 View 3D Structure Click here
B9FSH5 View 3D Structure Click here
D3ZX08 View 3D Structure Click here
F4IFC5 View 3D Structure Click here
I1J5B4 View 3D Structure Click here
I1JC08 View 3D Structure Click here
I1K6W0 View 3D Structure Click here
I1KMZ3 View 3D Structure Click here
I1LPK4 View 3D Structure Click here
I1NAJ0 View 3D Structure Click here
K7KHC2 View 3D Structure Click here
K7TY03 View 3D Structure Click here
O01541 View 3D Structure Click here
O04630 View 3D Structure Click here
O13914 View 3D Structure Click here
P00957 View 3D Structure Click here
P04801 View 3D Structure Click here
P0A8M3 View 3D Structure Click here
P26639 View 3D Structure Click here
P36428 View 3D Structure Click here
P40825 View 3D Structure Click here
P49588 View 3D Structure Click here
P50475 View 3D Structure Click here
P52709 View 3D Structure Click here
P53960 View 3D Structure Click here
P87144 View 3D Structure Click here
P9WFT5 View 3D Structure Click here
P9WFW7 View 3D Structure Click here
Q10A14 View 3D Structure Click here
Q14CH7 View 3D Structure Click here
Q1LVL3 View 3D Structure Click here
Q23122 View 3D Structure Click here
Q2FXP7 View 3D Structure Click here
Q2FXV9 View 3D Structure Click here
Q3THG9 View 3D Structure Click here
Q3UQ84 View 3D Structure Click here
Q4D4R0 View 3D Structure Click here
Q4D6L5 View 3D Structure Click here
Q4D747 View 3D Structure Click here
Q4D9G6 View 3D Structure Click here
Q4DPR0 View 3D Structure Click here
Q4DQ33 View 3D Structure Click here
Q54J66 View 3D Structure Click here
Q54Y20 View 3D Structure Click here
Q57984 View 3D Structure Click here
Q5A8K2 View 3D Structure Click here
Q5JTZ9 View 3D Structure Click here
Q5XHY5 View 3D Structure Click here
Q5XI17 View 3D Structure Click here
Q5XI97 View 3D Structure Click here
Q5ZDT9 View 3D Structure Click here
Q68FW7 View 3D Structure Click here
Q6DEJ5 View 3D Structure Click here
Q6ER90 View 3D Structure Click here
Q6Z0N5 View 3D Structure Click here
Q86H43 View 3D Structure Click here
Q8BGQ7 View 3D Structure Click here
Q8BLY2 View 3D Structure Click here
Q8ID31 View 3D Structure Click here
Q8IIA4 View 3D Structure Click here
Q9BTE6 View 3D Structure Click here
Q9BW92 View 3D Structure Click here
Q9D0R2 View 3D Structure Click here
Q9FFC7 View 3D Structure Click here
Q9VKB0 View 3D Structure Click here
Q9VLM8 View 3D Structure Click here
Q9VRJ1 View 3D Structure Click here
Q9W4R9 View 3D Structure Click here