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297  structures 8799  species 0  interactions 25665  sequences 185  architectures

Family: tRNA-synt_1b (PF00579)

Summary: tRNA synthetases class I (W and Y)

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tRNA synthetases class I (W and Y) Provide feedback

No Pfam abstract.

Literature references

  1. Doublie S, Bricogne G, Gilmore C, Carter CW Jr; , Structure 1995;3:17-31.: Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. PUBMED:7743129 EPMC:7743129


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002305

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...

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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
(37)
Full
(25665)
Representative proteomes UniProt
(107425)
RP15
(4209)
RP35
(12628)
RP55
(24504)
RP75
(39606)
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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
(37)
Full
(25665)
Representative proteomes UniProt
(107425)
RP15
(4209)
RP35
(12628)
RP55
(24504)
RP75
(39606)
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
(37)
Full
(25665)
Representative proteomes UniProt
(107425)
RP15
(4209)
RP35
(12628)
RP55
(24504)
RP75
(39606)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped 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: MRC-LMB Genome group
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A , Griffiths-Jones SR
Number in seed: 37
Number in full: 25665
Average length of the domain: 274.50 aa
Average identity of full alignment: 22 %
Average coverage of the sequence by the domain: 71.92 %

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 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 293
Family (HMM) version: 27
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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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_1b domain has been found. There are 297 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
A0A0G2KLM5 View 3D Structure Click here
A0A0P0VP63 View 3D Structure Click here
A0A0P0WGE6 View 3D Structure Click here
A0A0P0XCU4 View 3D Structure Click here
A0A0P0XEB2 View 3D Structure Click here
A0A144A140 View 3D Structure Click here
A0A1D6E966 View 3D Structure Click here
A0A1D6F7H2 View 3D Structure Click here
A0A1D6KWV1 View 3D Structure Click here
A0A1D6LHJ6 View 3D Structure Click here
A0A1D6LHJ7 View 3D Structure Click here
A0A1D6PW95 View 3D Structure Click here
A4HW83 View 3D Structure Click here
A4I070 View 3D Structure Click here
A4I443 View 3D Structure Click here
B0S5M9 View 3D Structure Click here
B4FMT8 View 3D Structure Click here
B6TBW5 View 3D Structure Click here
C0HKD6 View 3D Structure Click here
C0PCX3 View 3D Structure Click here
F1M8H2 View 3D Structure Click here
F1Q4R5 View 3D Structure Click here
F4HWL4 View 3D Structure Click here
F4HWL4 View 3D Structure Click here
G5ED95 View 3D Structure Click here
G5ED95 View 3D Structure Click here
G5EDY2 View 3D Structure Click here
G5EDY2 View 3D Structure Click here
H2KZL6 View 3D Structure Click here
I1J8W9 View 3D Structure Click here
I1JMN8 View 3D Structure Click here
I1K9G7 View 3D Structure Click here
I1LHP2 View 3D Structure Click here
I1LXN6 View 3D Structure Click here
K7KAB4 View 3D Structure Click here
K7KIY4 View 3D Structure Click here
K7M864 View 3D Structure Click here
O14055 View 3D Structure Click here
O42875 View 3D Structure Click here
O74890 View 3D Structure Click here
P00954 View 3D Structure Click here
P04803 View 3D Structure Click here
P0AGJ9 View 3D Structure Click here
P23381 View 3D Structure Click here
P32921 View 3D Structure Click here
P36421 View 3D Structure Click here
P48527 View 3D Structure Click here
P54577 View 3D Structure Click here
P9WFT1 View 3D Structure Click here
P9WFT3 View 3D Structure Click here
Q09692 View 3D Structure Click here
Q0KI98 View 3D Structure Click here
Q12109 View 3D Structure Click here
Q2FXJ5 View 3D Structure Click here
Q2FZQ7 View 3D Structure Click here
Q2QP62 View 3D Structure Click here
Q4CLY6 View 3D Structure Click here
Q4CPM2 View 3D Structure Click here
Q4CR77 View 3D Structure Click here
Q4CTS7 View 3D Structure Click here
Q4DE78 View 3D Structure Click here
Q4DE81 View 3D Structure Click here
Q4DSP6 View 3D Structure Click here
Q4KM49 View 3D Structure Click here
Q54WD9 View 3D Structure Click here
Q551A1 View 3D Structure Click here
Q55DZ8 View 3D Structure Click here
Q57834 View 3D Structure Click here
Q58810 View 3D Structure Click here
Q59WU2 View 3D Structure Click here
Q5A3P4 View 3D Structure Click here
Q5AFB3 View 3D Structure Click here
Q5AG80 View 3D Structure Click here
Q5I0L3 View 3D Structure Click here
Q5JKV2 View 3D Structure Click here
Q6P7B0 View 3D Structure Click here
Q6TGS6 View 3D Structure Click here
Q84PX0 View 3D Structure Click here
Q86A90 View 3D Structure Click here
Q86A90 View 3D Structure Click here
Q8BYL4 View 3D Structure Click here
Q8IAR7 View 3D Structure Click here
Q8IDW3 View 3D Structure Click here
Q8IIJ2 View 3D Structure Click here
Q8RXE9 View 3D Structure Click here
Q8S9J2 View 3D Structure Click here
Q91WQ3 View 3D Structure Click here
Q943W5 View 3D Structure Click here
Q9CYK1 View 3D Structure Click here
Q9M876 View 3D Structure Click here
Q9SR15 View 3D Structure Click here
Q9UGM6 View 3D Structure Click here
Q9VV60 View 3D Structure Click here
Q9VVL8 View 3D Structure Click here
Q9W107 View 3D Structure Click here
Q9Y2Z4 View 3D Structure Click here