Summary: tRNA synthetases class II (D, K and N)
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Aminoacyl tRNA synthetases, class II Edit Wikipedia article
|Aminoacyl-tRNA synthetase, class II|
Aminoacyl-tRNA synthetases, class II is a family of proteins. These proteins catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have a limited sequence homology.
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. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices, and are mostly dimeric or multimeric, containing at least three conserved regions. 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.
Human proteins containing this domain
- 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): 203â€“206. Bibcode:1990Natur.347..203E. doi:10.1038/347203a0. PMIDÂ 2203971. S2CIDÂ 4324290.
- 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): 197â€“208. doi:10.1016/S0969-2126(00)00095-2. PMIDÂ 10673435.
- Perona JJ, Steitz TA, Rould MA (1993). "Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase". Biochemistry. 32 (34): 8758â€“8771. doi:10.1021/bi00085a006. PMIDÂ 8364025.
- Delarue M, Moras D (1993). "The aminoacyl-tRNA synthetase family: modules at work". BioEssays. 15 (10): 675â€“687. doi:10.1002/bies.950151007. PMIDÂ 8274143. S2CIDÂ 35612984.
- Schimmel P (1991). "Classes of aminoacyl-tRNA synthetases and the establishment of the genetic code". Trends Biochem. Sci. 16 (1): 1â€“3. doi:10.1016/0968-0004(91)90002-D. PMIDÂ 2053131.
- Cusack S, Leberman R, Hartlein M (1991). "Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases". Nucleic Acids Res. 19 (13): 3489â€“3498. doi:10.1093/nar/19.13.3489. PMCÂ 328370. PMIDÂ 1852601.
- Bairoch A (2004). "List of aminoacyl-tRNA synthetases". Cite journal requires
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tRNA synthetases class II (D, K and N) Provide feedback
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Internal database links
|SCOOP:||AsnA GAD tRNA-synt_2b tRNA-synt_2d tRNA-synt_His tRNA_synthFbeta|
|Similarity to PfamA using HHSearch:||tRNA-synt_2d|
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.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||ATP binding (GO:0005524)|
|nucleotide binding (GO:0000166)|
|aminoacyl-tRNA ligase activity (GO:0004812)|
|Biological process||tRNA aminoacylation for protein translation (GO:0006418)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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  (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
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Author:||Bateman A , Sonnhammer ELL|
|Number in seed:||88|
|Number in full:||35280|
|Average length of the domain:||345.80 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||66.02 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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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 264 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.