Summary: Aminoacyl-tRNA editing domain
This is the Wikipedia entry entitled "YbaK protein domain". More...
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YbaK protein domain Edit Wikipedia article
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|YbaK protein domain|
Crystal structure of Cysteinyl-tRNA(Pro) deacylase protein from Haemophilus influenzae (hi1434)
In molecular biology, this protein domain of unknown function is found in numerous prokaryote organisms. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA.
Studies have shown that YbaK functions as a Cys-tRNAPro deacylase in vivo, deacetylation additionally involves turning genes off, hence, it can be assumed that it is preventing the addition of an amino acid to a tRNA molecule, thus preventing translation. In vitro studies with the full set of 20 E. coli aminoacyl-tRNAs revealed that the Haemophilus influenzae and E. coli YbaK proteins are moderately general aminoacyl-tRNA deacylases that preferentially hydrolyze Cys-tRNAPro and Cys-tRNACy. Furthermore, YbaK-mediated hydrolysis of aminoacyl-tRNA has been indicated to influence cell growth. It has been further indicated that YbaK domain is important in the editing function if the wrong amino acid has been joined to the wrong tRNA.
The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA. YbaK is a highly curved mixed seven-stranded beta-sheet surrounded by six short alpha helices 
- Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV et al. (2000). "Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.". Proteins 40 (1): 86–97. PMID 10813833.
- Ruan B, Söll D (2005). "The bacterial YbaK protein is a Cys-tRNAPro and Cys-tRNA Cys deacylase.". J Biol Chem 280 (27): 25887–91. doi:10.1074/jbc.M502174200. PMID 15886196.
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.
Aminoacyl-tRNA editing domain Provide feedback
This domain is found either on its own or in association with the tRNA synthetase class II core domain (PF00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro)[2-5]. The structure of this domain shows a novel fold .
Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O; , Proteins 2000;40:86-97.: Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. PUBMED:10813833 EPMC:10813833
So BR, An S, Kumar S, Das M, Turner DA, Hadad CM, Musier-Forsyth K;, J Biol Chem. 2011;286:31810-31820.: Substrate-mediated fidelity mechanism ensures accurate decoding of proline codons. PUBMED:21768119 EPMC:21768119
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR007214This domain of unknown function is found in numerous prokaryote organisms. The structure of YbaK shows a novel fold. This domain also occurs in a number of prolyl-tRNA synthetases (proRS) from prokaryotes. Thus, the domain is thought to be involved in oligonucleotide binding, with possible roles in recognition/discrimination or editing of prolyl-tRNA [PUBMED:10813833].
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Curation and family details
|Author:||Finn RD, Eberhardt R|
|Number in seed:||91|
|Number in full:||9872|
|Average length of the domain:||122.00 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||38.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||10|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
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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_edit domain has been found. There are 22 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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