1wn2

From Proteopedia

Crystal structure of project ID PH1539 from Pyrococcus horikoshii OT3

PDB ID 1wn2

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Structural highlights

1wn2 is a 1 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 1.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

PTH_PYRHO The natural substrate for this enzyme may be peptidyl-tRNAs which drop off the ribosome during protein synthesis (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

Peptidyl-tRNA hydrolases catalyze the hydrolytic removal of the peptidyl moiety from the peptidyl-tRNA molecule to prevent misreading during translation. Here, the expression, purification, crystallization and X-ray diffraction study of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3 (PhPth2) are described. The crystal structures were determined as similar biological dimers in two different forms: P4(1)2(1)2 at 1.2 A resolution (form 1) and P4(3)22 at 1.9 A resolution (form 2). In the form 1 structure, the asymmetric unit contains one PhPth2 subunit and a crystallographic twofold axis defines the dimeric association with the cognate subunit. In the form 2 structure, there are two PhPth2 subunits in the asymmetric unit that make a similar dimer with a noncrystallographic twofold axis. In order to evaluate the thermodynamic stability, the intra-protomer and inter-protomer interactions of PhPth2 were analyzed and compared with those of other Pth2-family members. The thermodynamic parameters show that the large number of ion pairs compared with family members from other mesophilic organisms would contribute to the thermostability of PhPth2. The structural difference between the two dimers was quantitatively evaluated by a multiple C(alpha)-atom superposition. A significant structural difference between the two dimers was observed around the putative active site of this enzyme. A rigid-body rotation takes place so as to retain the dimeric twofold symmetry, suggesting positive cooperativity upon tRNA binding. The mechanism of ligand binding was further investigated using a docking model with a tRNA molecule. The docking study suggests that the binding of tRNA requires its simultaneous interaction with both subunits of the PhPth2 dimer.

Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.,Shimizu K, Kuroishi C, Sugahara M, Kunishima N Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):444-53. Epub 2008, Mar 19. PMID:18391411^[1]

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

References

↑ Shimizu K, Kuroishi C, Sugahara M, Kunishima N. Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state. Acta Crystallogr D Biol Crystallogr. 2008 Apr;64(Pt 4):444-53. Epub 2008, Mar 19. PMID:18391411 doi:10.1107/S0907444908002850