9IX8

Crystallization and structural characterization of phosphopentomutase from the hyperthermophilic archaeon Thermococcus kodakarensis

Summary for 9IX8

• Entry DOI: 10.2210/pdb9ix8/pdb
• Descriptor: Phosphopentomutase, 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL, GLYCEROL, ... (4 entities in total)
• Functional Keywords: phosphopentomutase, thermococcus kodakarensis, hyperthermophilic archaea, phosphohexomutase homologue, isomerase
• Biological source: Thermococcus kodakarensis KOD1 (Pyrococcus kodakaraensis (strain KOD1))
• Total number of polymer chains: 4
• Total formula weight: 198579.63

Authors

Naz, Z.,Lubkowski, T.J.,Saleem, M.,Rahman, M.,Wlodawer, A.,Rashid, N. (deposition date: 2024-07-26, release date: 2024-12-18, Last modification date: 2025-01-01)

Primary citation

Naz, Z.,Lubkowski, J.,Saleem, M.,Aslam, M.,Rahman, M.,Wlodawer, A.,Rashid, N.
Biophysical Characterization of a Novel Phosphopentomutase from the Hyperthermophilic Archaeon Thermococcus kodakarensis .
Int J Mol Sci, 25:-, 2024

PubMed Abstract: Phosphopentomutases catalyze the isomerization of ribose 1-phosphate and ribose 5-phosphate. , a hyperthermophilic archaeon, harbors a novel enzyme (PPM) that exhibits high homology with phosphohexomutases but has no significant phosphohexomutase activity. Instead, PPM catalyzes the interconversion of ribose 1-phosphate and ribose 5-phosphate. Here, we report biophysical analysis, crystallization, and three-dimensional structure determination of PPM by X-ray diffraction at 2.39 Å resolution. The solved structure revealed a novel catalytic motif, unique to PPM, which makes this enzyme distinct from the homologous counterparts. We postulate that this novel catalytic motif may enable PPM to isomerize phosphopentose instead of phosphohexose. To the best of our knowledge, this is the first biophysical and structural analysis of a phosphopentomutase from hyperthermophilic archaea.

PubMed: 39684607
DOI: 10.3390/ijms252312893

Experimental method

X-RAY DIFFRACTION (2.39 Å)