Summary: Seryl-tRNA synthetase N-terminal domain
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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.
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
|SCOOP:||Herpes_U30 She9_MDM33 Phlebovirus_NSM CortBP2 Med30 YdfA_immunity TnpV Tox-ODYAM1 DUF4894 DAPDH_C|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015866
This entry represents the N-terminal domain of Serine-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Serine-tRNA synthetase (EC) exists as monomer and belongs to class IIa aminoacyl-tRNA synthetase [PUBMED:7540217].
The aminoacyl-tRNA synthetase (also known as aminoacyl-tRNA ligase) 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 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 and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases [PUBMED:]. 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.
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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
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Pfam-B_518 (release 5.4)|
|Author:||Mian N, Bateman A|
|Number in seed:||81|
|Number in full:||20819|
|Average length of the domain:||107.70 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||25.19 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
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There are 3 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 33 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 seqence.
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