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100  structures 8904  species 0  interactions 17947  sequences 126  architectures

Family: tRNA-synt_His (PF13393)

Summary: Histidyl-tRNA synthetase

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.

Histidyl-tRNA synthetase Provide feedback

This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits.

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR041715

HisRS is a homodimer and is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs [ PUBMED:12269828 ]. This domain is also found at the C terminus of eukaryotic GCN2 protein kinase [ PUBMED:7623840 ] and at the N terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain [ PUBMED:10430882 ].

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


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.

Representative proteomes UniProt
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PP/heatmap 1            

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

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

Format an alignment

Representative proteomes UniProt

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.

Representative proteomes UniProt
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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...


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: Jackhmmer:B0SA16
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 68
Number in full: 17947
Average length of the domain: 288.6 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 56.61 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.0 25.0
Noise cut-off 24.9 24.9
Model length: 309
Family (HMM) version: 9
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


Generate a FASTA-format file

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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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The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


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_His domain has been found. There are 100 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
A0A044R448 View 3D Structure Click here
A0A044SXE6 View 3D Structure Click here
A0A077ZG45 View 3D Structure Click here
A0A077ZI64 View 3D Structure Click here
A0A077ZJD7 View 3D Structure Click here
A0A0D2E169 View 3D Structure Click here
A0A0D2ENY3 View 3D Structure Click here
A0A0H3H1G0 View 3D Structure Click here
A0A0I9N5H6 View 3D Structure Click here
A0A0K0E1K2 View 3D Structure Click here
A0A0N4UI79 View 3D Structure Click here
A0A0R0KPW1 View 3D Structure Click here
A0A0R0KYN0 View 3D Structure Click here
A0A175W717 View 3D Structure Click here
A0A175WIG8 View 3D Structure Click here
A0A1C1CL38 View 3D Structure Click here
A0A1C1CPU1 View 3D Structure Click here
A0A1D6E7D5 View 3D Structure Click here
A0A1D6FUK0 View 3D Structure Click here
A0A1D6LIU0 View 3D Structure Click here
A0A1D6MIP9 View 3D Structure Click here
A0A1D8PQT9 View 3D Structure Click here
A0A3P7GEH8 View 3D Structure Click here
A0A3Q0KDC5 View 3D Structure Click here
A0A5S6PAX9 View 3D Structure Click here
A0KJ45 View 3D Structure Click here
A0PXP2 View 3D Structure Click here
A0PZW9 View 3D Structure Click here
A1ANS7 View 3D Structure Click here
A1AWV6 View 3D Structure Click here
A1B3C5 View 3D Structure Click here
A1BDE6 View 3D Structure Click here
A1K3Z0 View 3D Structure Click here
A1K3Z9 View 3D Structure Click here
A1S862 View 3D Structure Click here
A1T898 View 3D Structure Click here
A1TM36 View 3D Structure Click here
A1UTY3 View 3D Structure Click here
A1W578 View 3D Structure Click here
A1W587 View 3D Structure Click here