YbaK protein domain

Protein domain

YbaK protein domain

Crystal structure of Cysteinyl-tRNA(Pro) deacylase protein from Haemophilus influenzae (hi1434)

Identifiers
Symbol| YbaK
Pfam| PF04073
InterPro| IPR007214
SCOP2| 1dbx / SCOPe / SUPFAM
CDD| cd04332
| Available protein structures:

Pfam  | structures / ECOD
PDB| RCSB PDB; PDBe; PDBj
PDBsum| structure summary

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.[1]

## Function

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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.[2] 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.

## Structure

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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[1]

## References

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1. ^ a b 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\. doi:10.1002/(sici)1097-0134(20000701)40:1<86::aid-prot100>3.0.co;2-y. PMID 10813833. S2CID 12319834.
2. ^ 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 article incorporates text from the public domain Pfam and InterPro: IPR007214