2dq0

From Proteopedia

Crystal structure of seryl-tRNA synthetase from Pyrococcus horikoshii complexed with a seryl-adenylate analog

PDB ID 2dq0

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Structural highlights

2dq0 is a 2 chain structure with sequence from Pyrococcus horikoshii OT3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

SYS_PYRHO Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec) (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS from the archaeon Pyrococcus horikoshii bound with 5'-O-[N-(L-seryl)-sulfamoyl]-adenosine at 2.6 A and with ATP at 2.8 A, as well as in the apo form at 3.0 A. P. horikoshii SerRS recognizes the seryl and adenylate moieties in a manner similar to those of the bacterial and mitochondrial SerRSs from Thermus thermophilus and Bos taurus, respectively, but different from that of the unusual SerRS from the methanogenic archaeon Methanosarcina barkeri. P. horikoshii SerRS efficiently aminoacylated not only P. horikoshii tRNA(Ser) but also bacterial tRNA(Ser)s from T. thermophilus and Escherichia coli. Models of P. horikoshii SerRS bound with the T. thermophilus and P. horikoshii tRNA(Ser)s suggested that the helical domain of P. horikoshii SerRS is involved in the extra arm binding. This region of P. horikoshii SerRS has additional basic residues as compared with T. thermophilus SerRS, and a Trp residue specific to the archaeal/eukaryal SerRSs. Mutational analyses revealed that the basic and Trp residues are important for tRNA aminoacylation. P. horikoshii SerRS has the archaea-specific insertion, which collaborates with the core domain to form a basic channel leading to the active site. Two sulfate ions are bound to the channel, suggesting that the tRNA 3' region might bind to the channel.

Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii.,Itoh Y, Sekine SI, Kuroishi C, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S RNA Biol. 2008 Jul 28;5(3). PMID:18818520^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Itoh Y, Sekine SI, Kuroishi C, Terada T, Shirouzu M, Kuramitsu S, Yokoyama S. Crystallographic and mutational studies of seryl-tRNA synthetase from the archaeon Pyrococcus horikoshii. RNA Biol. 2008 Jul 28;5(3). PMID:18818520