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198  structures 8807  species 0  interactions 44063  sequences 382  architectures

Family: tRNA-synt_1 (PF00133)

Summary: tRNA synthetases class I (I, L, M and V)

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tRNA synthetases class I (I, L, M and V) Provide feedback

Other tRNA synthetase sub-families are too dissimilar to be included.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002300

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 ].

The class Ia aminoacyl-tRNA synthetases consist of the isoleucyl, methionyl, valyl, leucyl, cysteinyl, and arginyl-tRNA synthetases; the class Ib include the glutamyl and glutaminyl-tRNA synthetases, and the class Ic are the tyrosyl and tryptophanyl-tRNA synthetases [ PUBMED:11590011 ].

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 HUP (CL0039), which has the following description:

The HUP class contains the HIGH-signature proteins, UspA superfamily and the PP-ATPase superfamily [1]. The HIGH superfamily has the HIGH Nucleotidyl transferases and the class I tRNA synthetases both of which have the HIGH and the KMSKS motif [1],[2]. The PP-loop ATPase named after the ATP PyroPhosphatase domain, was initially identified as a conserved amino acid sequence motif in four distinct groups of enzymes that catalyse the hydrolysis of the alpha-beta phosphate bond of ATP, namely GMP synthetases, argininosuccinate synthetases, asparagine synthetases, and ATP sulfurylases [3]. The USPA superfamily contains USPA, ETFP and Photolyases [1]

The clan contains the following 31 members:

Arginosuc_synth Asn_synthase ATP-sulfurylase ATP_bind_3 BshC CDPS Citrate_ly_lig CTP_transf_like Diphthami_syn_2 DNA_photolyase DPRP ETF FAD_syn HIGH_NTase1 HIGH_NTase1_ass NAD_synthase Pantoate_ligase PAPS_reduct QueC ThiI tRNA-synt_1 tRNA-synt_1_2 tRNA-synt_1b tRNA-synt_1c tRNA-synt_1d tRNA-synt_1e tRNA-synt_1f tRNA-synt_1g tRNA_Me_trans UDPG_MGDP_dh_C Usp

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
(11)
Full
(44063)
Representative proteomes UniProt
(191824)
RP15
(7234)
RP35
(21473)
RP55
(41824)
RP75
(66833)
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
(11)
Full
(44063)
Representative proteomes UniProt
(191824)
RP15
(7234)
RP35
(21473)
RP55
(41824)
RP75
(66833)
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
(11)
Full
(44063)
Representative proteomes UniProt
(191824)
RP15
(7234)
RP35
(21473)
RP55
(41824)
RP75
(66833)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Sonnhammer ELL
Number in seed: 11
Number in full: 44063
Average length of the domain: 390.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 54.35 %

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 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 602
Family (HMM) version: 24
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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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-synt_1 domain has been found. There are 198 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
A0A0B4KF06 View 3D Structure Click here
A0A0G2JZH2 View 3D Structure Click here
A0A0G2K261 View 3D Structure Click here
A0A0G2K9E5 View 3D Structure Click here
A0A0G2K9E5 View 3D Structure Click here
A0A0G2K9E5 View 3D Structure Click here
A0A0P0UX97 View 3D Structure Click here
A0A0P0VFN6 View 3D Structure Click here
A0A0P0VX51 View 3D Structure Click here
A0A0P0XWD3 View 3D Structure Click here
A0A0R0FH81 View 3D Structure Click here
A0A0R0FH81 View 3D Structure Click here
A0A0R0FN16 View 3D Structure Click here
A0A0R0FNA1 View 3D Structure Click here
A0A0R0FQB9 View 3D Structure Click here
A0A0R0I5G1 View 3D Structure Click here
A0A1D6DUN1 View 3D Structure Click here
A0A1D6DUN1 View 3D Structure Click here
A0A1D6EBD9 View 3D Structure Click here
A0A1D6ENT5 View 3D Structure Click here
A0A1D6ENT5 View 3D Structure Click here
A0A1D6EUI9 View 3D Structure Click here
A0A1D6F9V3 View 3D Structure Click here
A0A1D6FD95 View 3D Structure Click here
A0A1D6FD95 View 3D Structure Click here
A0A1D6FGW0 View 3D Structure Click here
A0A1D6HM00 View 3D Structure Click here
A0A1D6HM00 View 3D Structure Click here
A0A1D6IZJ9 View 3D Structure Click here
A0A1D6IZK0 View 3D Structure Click here
A0A1D6K8N4 View 3D Structure Click here
A0A1D6LFD2 View 3D Structure Click here
A0A1D6LQQ9 View 3D Structure Click here
A0A1D6P365 View 3D Structure Click here
A0A1D8PHR0 View 3D Structure Click here
A0A1D8PQ56 View 3D Structure Click here
A0A1D8PS12 View 3D Structure Click here
A0A1D8PS12 View 3D Structure Click here
A0A1D8PSG5 View 3D Structure Click here
A0A1X7YIU4 View 3D Structure Click here
A4HVN8 View 3D Structure Click here
A4HVN8 View 3D Structure Click here
A4I5Z4 View 3D Structure Click here
A4IDX6 View 3D Structure Click here
C6KT64 View 3D Structure Click here
C6KT64 View 3D Structure Click here
E2JL04 View 3D Structure Click here
E7F9F1 View 3D Structure Click here
E7F9F1 View 3D Structure Click here
F1LS86 View 3D Structure Click here
F1Q740 View 3D Structure Click here
F1QFN3 View 3D Structure Click here
F1QSW0 View 3D Structure Click here
F1QSY7 View 3D Structure Click here
F1QUQ0 View 3D Structure Click here
F1R7M6 View 3D Structure Click here
F1R7M6 View 3D Structure Click here
F1R7M6 View 3D Structure Click here
F4I116 View 3D Structure Click here
F4I116 View 3D Structure Click here
F4J2W0 View 3D Structure Click here
F4JLM5 View 3D Structure Click here
F4JLM5 View 3D Structure Click here
F4KE63 View 3D Structure Click here
I1J9U5 View 3D Structure Click here
I1J9U5 View 3D Structure Click here
I1KNG6 View 3D Structure Click here
I1LGR6 View 3D Structure Click here
I1LGR6 View 3D Structure Click here
I1LIK8 View 3D Structure Click here
I1LIK8 View 3D Structure Click here
I1LPC3 View 3D Structure Click here
I1LPC3 View 3D Structure Click here
I1MRI5 View 3D Structure Click here
K7N3M6 View 3D Structure Click here
K7WAM2 View 3D Structure Click here
O13651 View 3D Structure Click here
O14160 View 3D Structure Click here
O75005 View 3D Structure Click here
O77354 View 3D Structure Click here
O77354 View 3D Structure Click here
P00956 View 3D Structure Click here
P07118 View 3D Structure Click here
P07806 View 3D Structure Click here
P07813 View 3D Structure Click here
P07813 View 3D Structure Click here
P07813 View 3D Structure Click here
P09436 View 3D Structure Click here
P11325 View 3D Structure Click here
P26637 View 3D Structure Click here
P26637 View 3D Structure Click here
P26640 View 3D Structure Click here
P41252 View 3D Structure Click here
P48526 View 3D Structure Click here
P93736 View 3D Structure Click here
P9WFS9 View 3D Structure Click here
P9WFS9 View 3D Structure Click here
P9WFV3 View 3D Structure Click here
Q04462 View 3D Structure Click here
Q09828 View 3D Structure Click here
Q09828 View 3D Structure Click here
Q09828 View 3D Structure Click here
Q09996 View 3D Structure Click here
Q09996 View 3D Structure Click here
Q0J0N6 View 3D Structure Click here
Q0J0N6 View 3D Structure Click here
Q10490 View 3D Structure Click here
Q10490 View 3D Structure Click here
Q15031 View 3D Structure Click here
Q15031 View 3D Structure Click here
Q15031 View 3D Structure Click here
Q21926 View 3D Structure Click here
Q23360 View 3D Structure Click here
Q23511 View 3D Structure Click here
Q2FXH2 View 3D Structure Click here
Q2FXR8 View 3D Structure Click here
Q2FZ82 View 3D Structure Click here
Q3U2A8 View 3D Structure Click here
Q4CL52 View 3D Structure Click here
Q4CPJ9 View 3D Structure Click here
Q4CTR0 View 3D Structure Click here
Q4CTR0 View 3D Structure Click here
Q4D2F2 View 3D Structure Click here
Q4DQQ7 View 3D Structure Click here
Q54CE4 View 3D Structure Click here
Q54ET5 View 3D Structure Click here
Q54I78 View 3D Structure Click here
Q54N83 View 3D Structure Click here
Q54N83 View 3D Structure Click here
Q54YD4 View 3D Structure Click here
Q58050 View 3D Structure Click here
Q58357 View 3D Structure Click here
Q58413 View 3D Structure Click here
Q59RI1 View 3D Structure Click here
Q5PPJ6 View 3D Structure Click here
Q5PPJ6 View 3D Structure Click here
Q5ST30 View 3D Structure Click here
Q60EV0 View 3D Structure Click here
Q67WM2 View 3D Structure Click here
Q6H4P7 View 3D Structure Click here
Q6H4P7 View 3D Structure Click here
Q6MG21 View 3D Structure Click here
Q6ZGC2 View 3D Structure Click here
Q851K9 View 3D Structure Click here
Q86KU2 View 3D Structure Click here
Q8BIJ6 View 3D Structure Click here
Q8BMJ2 View 3D Structure Click here
Q8BMJ2 View 3D Structure Click here
Q8BU30 View 3D Structure Click here
Q8I5G6 View 3D Structure Click here
Q8I5G6 View 3D Structure Click here
Q8I5G6 View 3D Structure Click here
Q8I5G6 View 3D Structure Click here
Q8IBB3 View 3D Structure Click here
Q8IBB3 View 3D Structure Click here
Q8IBB3 View 3D Structure Click here
Q8IDZ9 View 3D Structure Click here
Q8IDZ9 View 3D Structure Click here
Q8IKL5 View 3D Structure Click here
Q8MSW0 View 3D Structure Click here
Q8RXK8 View 3D Structure Click here
Q8VDC0 View 3D Structure Click here
Q8VDC0 View 3D Structure Click here
Q8VDC0 View 3D Structure Click here
Q9NSE4 View 3D Structure Click here
Q9P2J5 View 3D Structure Click here
Q9P2J5 View 3D Structure Click here
Q9U1Q4 View 3D Structure Click here
Q9USL3 View 3D Structure Click here
Q9VQR8 View 3D Structure Click here
Q9VQR8 View 3D Structure Click here
Q9VSR7 View 3D Structure Click here
Q9VUY4 View 3D Structure Click here
Q9VZ82 View 3D Structure Click here
Q9XEA0 View 3D Structure Click here
Q9Z1Q9 View 3D Structure Click here