YbaK protein domain

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

YbaK protein domain
	Crystal structure of Cysteinyl-tRNA(Pro) deacylase protein from Haemophilus influenzae (hi1434)
Identifiers
Symbol	YbaK
Pfam	PF04073
InterPro	IPR007214
SCOPe	1dbx / 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

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

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]

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References

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.
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

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[pmid10813833-1] 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.

[pmid15886196-2] 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.