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252  structures 8792  species 0  interactions 33408  sequences 279  architectures

Family: tRNA-synt_2 (PF00152)

Summary: tRNA synthetases class II (D, K and N)

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This is the Wikipedia entry entitled "Aminoacyl tRNA synthetases, class II". More...

Aminoacyl tRNA synthetases, class II Edit Wikipedia article

Aminoacyl-tRNA synthetase, class II (D, K and N)
Identifiers
Symbolaa-tRNA-synt_II
PfamPF00152
InterProIPR004364
CDDcd00768

Aminoacyl-tRNA synthetase, class II (D, K and N) is a protein domain that catalyses the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. This protein differs widely in size and oligomeric state, and has a limited sequence homology.[1]

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.[2] Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices,[3] and are mostly dimeric or multimeric, containing at least three conserved regions.[4][5][6] 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 and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases.[7]

Human proteins containing this domain

References

  1. ^ Delarue M, Moras D, Poch O, Eriani G, Gangloff J (1990). "Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs". Nature. 347 (6289): 203–206. doi:10.1038/347203a0. PMID 2203971.
  2. ^ Moras D, Konno M, Shimada A, Nureki O, Tateno M, Yokoyama S, Sugiura I, Ugaji-Yoshikawa Y, Kuwabara S, Lorber B, Giege R (2000). "The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules". Structure. 8 (2): 197–208. doi:10.1016/S0969-2126(00)00095-2. PMID 10673435.
  3. ^ Perona JJ, Steitz TA, Rould MA (1993). "Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase". Biochemistry. 32 (34): 8758–8771. doi:10.1021/bi00085a006. PMID 8364025.
  4. ^ Delarue M, Moras D (1993). "The aminoacyl-tRNA synthetase family: modules at work". BioEssays. 15 (10): 675–687. doi:10.1002/bies.950151007. PMID 8274143.
  5. ^ Schimmel P (1991). "Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code". Trends Biochem. Sci. 16 (1): 1–3. doi:10.1016/0968-0004(91)90002-D. PMID 2053131.
  6. ^ Cusack S, Leberman R, Hartlein M (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases". Nucleic Acids Res. 19 (13): 3489–3498. doi:10.1093/nar/19.13.3489. PMC 328370. PMID 1852601.
  7. ^ Bairoch A (2004). "List of aminoacyl-tRNA synthetases": –. Cite journal requires |journal= (help)
This article incorporates text from the public domain Pfam and InterPro: IPR004364

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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tRNA synthetases class II (D, K and N) Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004364

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 includes the asparagine, aspartic acid and lysine tRNA synthetases.

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 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

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
(88)
Full
(33408)
Representative proteomes UniProt
(136378)
RP15
(5524)
RP35
(16539)
RP55
(31295)
RP75
(50112)
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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
(88)
Full
(33408)
Representative proteomes UniProt
(136378)
RP15
(5524)
RP35
(16539)
RP55
(31295)
RP75
(50112)
Alignment:
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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
(88)
Full
(33408)
Representative proteomes UniProt
(136378)
RP15
(5524)
RP35
(16539)
RP55
(31295)
RP75
(50112)
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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Sonnhammer ELL
Number in seed: 88
Number in full: 33408
Average length of the domain: 345.10 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 66.06 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 314
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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_2 domain has been found. There are 252 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
A0A0G2K7D7 View 3D Structure Click here
A0A0P0VEM7 View 3D Structure Click here
A0A0P0X6F8 View 3D Structure Click here
A0A0R0FPU3 View 3D Structure Click here
A0A0R0FYI1 View 3D Structure Click here
A0A0R0I6W2 View 3D Structure Click here
A0A0R0IKR4 View 3D Structure Click here
A0A0R0J805 View 3D Structure Click here
A0A0R4IAS3 View 3D Structure Click here
A0A1D6EHY1 View 3D Structure Click here
A0A1D6EVR1 View 3D Structure Click here
A0A1D6FGX9 View 3D Structure Click here
A0A1D6FII0 View 3D Structure Click here
A0A1D6FII0 View 3D Structure Click here
A0A1D6GM16 View 3D Structure Click here
A0A1D6IBP5 View 3D Structure Click here
A0A1D6KWD0 View 3D Structure Click here
A0A1D6LAP1 View 3D Structure Click here
A0A1D6LAQ0 View 3D Structure Click here
A0A1D6ML85 View 3D Structure Click here
A0A1D6QC90 View 3D Structure Click here
A0A1D8PD81 View 3D Structure Click here
A0A1D8PQY7 View 3D Structure Click here
A4HWC4 View 3D Structure Click here
A4I508 View 3D Structure Click here
A4I574 View 3D Structure Click here
A4IA13 View 3D Structure Click here
B8A5D3 View 3D Structure Click here
C0P4T5 View 3D Structure Click here
E7FA20 View 3D Structure Click here
E9AGV6 View 3D Structure Click here
E9QFP3 View 3D Structure Click here
F1LPV0 View 3D Structure Click here
F1R246 View 3D Structure Click here
F4J7V2 View 3D Structure Click here
F4JJT9 View 3D Structure Click here
F7ESZ5 View 3D Structure Click here
F7ESZ5 View 3D Structure Click here
I1JMN9 View 3D Structure Click here
I1K0Q4 View 3D Structure Click here
I1K5N2 View 3D Structure Click here
I1K622 View 3D Structure Click here
I1K622 View 3D Structure Click here
I1KPU2 View 3D Structure Click here
I1KPU2 View 3D Structure Click here
I1L9B1 View 3D Structure Click here
I1LZI3 View 3D Structure Click here
I1M984 View 3D Structure Click here
I1MM63 View 3D Structure Click here
I1MM63 View 3D Structure Click here
I1MV15 View 3D Structure Click here
I1MX58 View 3D Structure Click here
K7KDX4 View 3D Structure Click here
K7KDX4 View 3D Structure Click here
K7MJN5 View 3D Structure Click here
M9PDL2 View 3D Structure Click here
O43776 View 3D Structure Click here
O48593 View 3D Structure Click here
O74407 View 3D Structure Click here
O74858 View 3D Structure Click here
O94242 View 3D Structure Click here
O94567 View 3D Structure Click here
O96198 View 3D Structure Click here
O96198 View 3D Structure Click here
P04802 View 3D Structure Click here
P0A8M0 View 3D Structure Click here
P0A8N3 View 3D Structure Click here
P0A8N5 View 3D Structure Click here
P0A8N7 View 3D Structure Click here
P14868 View 3D Structure Click here
P15178 View 3D Structure Click here
P15179 View 3D Structure Click here
P15180 View 3D Structure Click here
P21889 View 3D Structure Click here
P25345 View 3D Structure Click here
P32048 View 3D Structure Click here
P38707 View 3D Structure Click here
P90831 View 3D Structure Click here
P9WFU7 View 3D Structure Click here
P9WFU9 View 3D Structure Click here
P9WFW3 View 3D Structure Click here
Q03577 View 3D Structure Click here
Q0JQL0 View 3D Structure Click here
Q15046 View 3D Structure Click here
Q19722 View 3D Structure Click here
Q22099 View 3D Structure Click here
Q2FXU5 View 3D Structure Click here
Q2FYH6 View 3D Structure Click here
Q2G0Q3 View 3D Structure Click here
Q2QSX5 View 3D Structure Click here
Q2QSX5 View 3D Structure Click here
Q3KRD0 View 3D Structure Click here
Q4CNC1 View 3D Structure Click here
Q4CRU7 View 3D Structure Click here
Q4CWW7 View 3D Structure Click here
Q4D7V3 View 3D Structure Click here
Q4DLP1 View 3D Structure Click here
Q4DQH8 View 3D Structure Click here
Q4DTR8 View 3D Structure Click here
Q4E595 View 3D Structure Click here
Q54LP4 View 3D Structure Click here
Q54TY4 View 3D Structure Click here
Q554D9 View 3D Structure Click here
Q559M9 View 3D Structure Click here
Q55C99 View 3D Structure Click here
Q55FI3 View 3D Structure Click here
Q58950 View 3D Structure Click here
Q59R18 View 3D Structure Click here
Q59R23 View 3D Structure Click here
Q59UF7 View 3D Structure Click here
Q5ADU2 View 3D Structure Click here
Q5XIM7 View 3D Structure Click here
Q6DHE6 View 3D Structure Click here
Q6F2U9 View 3D Structure Click here
Q6K1T2 View 3D Structure Click here
Q6PI48 View 3D Structure Click here
Q6ZHC3 View 3D Structure Click here
Q75JQ1 View 3D Structure Click here
Q7JZR5 View 3D Structure Click here
Q7K0E6 View 3D Structure Click here
Q8BGV0 View 3D Structure Click here
Q8BIP0 View 3D Structure Click here
Q8BP47 View 3D Structure Click here
Q8H104 View 3D Structure Click here
Q8I2B1 View 3D Structure Click here
Q8I3W4 View 3D Structure Click here
Q8I408 View 3D Structure Click here
Q8I408 View 3D Structure Click here
Q8IDJ8 View 3D Structure Click here
Q8ILS8 View 3D Structure Click here
Q8ILS8 View 3D Structure Click here
Q922B2 View 3D Structure Click here
Q93WM3 View 3D Structure Click here
Q93WM3 View 3D Structure Click here
Q95PZ8 View 3D Structure Click here
Q96I59 View 3D Structure Click here
Q99MN1 View 3D Structure Click here
Q9LJE2 View 3D Structure Click here
Q9M084 View 3D Structure Click here
Q9M9C7 View 3D Structure Click here
Q9P6I0 View 3D Structure Click here
Q9SSK1 View 3D Structure Click here
Q9SSK1 View 3D Structure Click here
Q9SW95 View 3D Structure Click here
Q9SW96 View 3D Structure Click here
Q9SW96 View 3D Structure Click here
Q9UUE6 View 3D Structure Click here
Q9V434 View 3D Structure Click here
Q9W327 View 3D Structure Click here
Q9ZPI1 View 3D Structure Click here