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75  structures 8730  species 0  interactions 11266  sequences 72  architectures

Family: Seryl_tRNA_N (PF02403)

Summary: Seryl-tRNA synthetase N-terminal domain

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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.

Seryl-tRNA synthetase N-terminal domain Provide feedback

This domain is found associated with the Pfam tRNA synthetase class II domain (PF00587) and represents the N-terminal domain of seryl-tRNA synthetase.

Literature references

  1. Cusack S, Yaremchuk A, Tukalo M; , EMBO J 1996;15:2834-2842.: The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. PUBMED:8654381 EPMC:8654381


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015866

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 entry represents the N-terminal domain of Serine-tRNA synthetase, which consists of two helices in a long alpha-hairpin and corresponds to the tRNA binding domain. Serine-tRNA synthetase ( EC ) exists as monomer and belongs to class IIa aminoacyl-tRNA synthetase [ PUBMED:7540217 ].

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_bind_arm (CL0298), which has the following description:

This domain is found in Phe and Ser tRNA synthetases at the N-terminus, and at the C-terminus of Val tRNA synthetase. The domain is composed of two helices.

The clan contains the following 3 members:

Phe_tRNA-synt_N Seryl_tRNA_N Val_tRNA-synt_C

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
(78)
Full
(11266)
Representative proteomes UniProt
(48421)
RP15
(1777)
RP35
(5603)
RP55
(10948)
RP75
(17959)
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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

  Seed
(78)
Full
(11266)
Representative proteomes UniProt
(48421)
RP15
(1777)
RP35
(5603)
RP55
(10948)
RP75
(17959)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(78)
Full
(11266)
Representative proteomes UniProt
(48421)
RP15
(1777)
RP35
(5603)
RP55
(10948)
RP75
(17959)
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_518 (release 5.4)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 78
Number in full: 11266
Average length of the domain: 108.5 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 24.34 %

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 28.2 28.2
Trusted cut-off 28.2 28.2
Noise cut-off 28.1 28.1
Model length: 108
Family (HMM) version: 25
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 Seryl_tRNA_N domain has been found. There are 75 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
A0A044V4I8 View 3D Structure Click here
A0A077Z5R4 View 3D Structure Click here
A0A0D2E260 View 3D Structure Click here
A0A0D2G9N5 View 3D Structure Click here
A0A0H3GQM5 View 3D Structure Click here
A0A0K0EEG0 View 3D Structure Click here
A0A0N4U869 View 3D Structure Click here
A0A175WDN5 View 3D Structure Click here
A0A175WEZ6 View 3D Structure Click here
A0A1C1D284 View 3D Structure Click here
A0A1D6JH90 View 3D Structure Click here
A0A1D6PQL3 View 3D Structure Click here
A0A1X7YED1 View 3D Structure Click here
A0A5K4EE55 View 3D Structure Click here
A0JR71 View 3D Structure Click here
A0KJE8 View 3D Structure Click here
A0L6J8 View 3D Structure Click here
A0LI63 View 3D Structure Click here
A0LWR6 View 3D Structure Click here
A0Q3T2 View 3D Structure Click here
A0R638 View 3D Structure Click here
A0RTS8 View 3D Structure Click here
A1A0B7 View 3D Structure Click here
A1ALM7 View 3D Structure Click here
A1B4S2 View 3D Structure Click here
A1BHA5 View 3D Structure Click here
A1K581 View 3D Structure Click here
A1R120 View 3D Structure Click here
A1S6H5 View 3D Structure Click here
A1SD34 View 3D Structure Click here
A1SVE4 View 3D Structure Click here
A1TGX4 View 3D Structure Click here
A1TTM6 View 3D Structure Click here
A1UN98 View 3D Structure Click here
A1US81 View 3D Structure Click here
A1VSK4 View 3D Structure Click here
A1WBD4 View 3D Structure Click here
A1WP10 View 3D Structure Click here
A1WWU7 View 3D Structure Click here
A2BM70 View 3D Structure Click here