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11  structures 8628  species 0  interactions 12802  sequences 83  architectures

Family: tRNA-synt_1e (PF01406)

Summary: tRNA synthetases class I (C) catalytic 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.

tRNA synthetases class I (C) catalytic domain Provide feedback

This family includes only cysteinyl tRNA synthetases.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR032678

This entry represents the catalytic (Rossmann-fold) domain found in cysteinyl tRNA synthetases [ PUBMED:22184460 ] which is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding.

Cysteine-tRNA ligase (also known as cysteinyl-tRNA synthetase) ( EC ) is an alpha monomer and belongs to class Ia [ PUBMED:1992490 ]. It aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. It is highly specific despite not possessing the amino acid editing activity characteristic of many other tRNA ligases [ PUBMED:12032090 , PUBMED:10704480 , PUBMED:12458790 , PUBMED:10447505 , PUBMED:7647112 , PUBMED:14665676 , PUBMED:7783224 , PUBMED:11550797 , PUBMED:11310981 , PUBMED:8274143 , PUBMED:2203971 , PUBMED:7479698 ].

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
(10)
Full
(12802)
Representative proteomes UniProt
(55595)
RP15
(1935)
RP35
(6245)
RP55
(12402)
RP75
(20064)
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
(10)
Full
(12802)
Representative proteomes UniProt
(55595)
RP15
(1935)
RP35
(6245)
RP55
(12402)
RP75
(20064)
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
(10)
Full
(12802)
Representative proteomes UniProt
(55595)
RP15
(1935)
RP35
(6245)
RP55
(12402)
RP75
(20064)
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: Swissprot
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Howe K , Bateman A
Number in seed: 10
Number in full: 12802
Average length of the domain: 308.30 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 61.48 %

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 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 301
Family (HMM) version: 21
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_1e domain has been found. There are 11 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
A0A0N7KGK1 View 3D Structure Click here
A0A0N7KRW9 View 3D Structure Click here
A0A0R0EM71 View 3D Structure Click here
A0A0R0I6U8 View 3D Structure Click here
A0A0R0J6F1 View 3D Structure Click here
A0A143ZXE7 View 3D Structure Click here
A0A143ZZ50 View 3D Structure Click here
A0A1D6JEF6 View 3D Structure Click here
A0A1D6LAG9 View 3D Structure Click here
A0A1D6M5V5 View 3D Structure Click here
A0A1D6M5V5 View 3D Structure Click here
A0A1D6NG98 View 3D Structure Click here
B2GV57 View 3D Structure Click here
B3LFA4 View 3D Structure Click here
B4FD20 View 3D Structure Click here
C0PHQ1 View 3D Structure Click here
E7FC09 View 3D Structure Click here
E7FDV9 View 3D Structure Click here
E9AGB4 View 3D Structure Click here
F4IPY2 View 3D Structure Click here
G3V9K0 View 3D Structure Click here
I1K8S4 View 3D Structure Click here
K7KIH3 View 3D Structure Click here
O76618 View 3D Structure Click here
P21888 View 3D Structure Click here
P49589 View 3D Structure Click here
P53852 View 3D Structure Click here
P9WFW1 View 3D Structure Click here
P9WJM9 View 3D Structure Click here
Q09860 View 3D Structure Click here
Q0IZQ2 View 3D Structure Click here
Q2G2M6 View 3D Structure Click here
Q4CQ34 View 3D Structure Click here
Q4CUZ9 View 3D Structure Click here
Q54KR1 View 3D Structure Click here
Q54ZY3 View 3D Structure Click here
Q5AL46 View 3D Structure Click here
Q7K3P0 View 3D Structure Click here
Q7KN90 View 3D Structure Click here
Q8BYM8 View 3D Structure Click here
Q8IJP3 View 3D Structure Click here
Q9ER72 View 3D Structure Click here
Q9HA77 View 3D Structure Click here
Q9LYL3 View 3D Structure Click here