5ETJ

Crystal structure of purine nucleoside phosphorylase (E258D, L261A) mutant from human complexed with DADMe-ImmG and phosphate

Summary for 5ETJ

• Entry DOI: 10.2210/pdb5etj/pdb
• Related: 3PHB
• Descriptor: Purine nucleoside phosphorylase, 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: phosphorylase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 6
• Total formula weight: 219367.79

Authors

Cameron, S.A.,Suarez, J.,Schramm, V.L.,Almo, S.C. (deposition date: 2015-11-17, release date: 2016-09-14, Last modification date: 2023-09-27)

Primary citation

Zoi, I.,Suarez, J.,Antoniou, D.,Cameron, S.A.,Schramm, V.L.,Schwartz, S.D.
Modulating Enzyme Catalysis through Mutations Designed to Alter Rapid Protein Dynamics.
J.Am.Chem.Soc., 138:3403-3409, 2016

PubMed Abstract: The relevance of sub-picosecond protein motions to the catalytic event remains a topic of debate. Heavy enzymes (isotopically substituted) provide an experimental tool for bond-vibrational links to enzyme catalysis. A recent transition path sampling study with heavy purine nucleoside phosphorylase (PNP) characterized the experimentally observed mass-dependent slowing of barrier crossing (Antoniou, D.; Ge, X.; Schramm, V. L.; Schwartz, S. D. J. Phys. Chem. Lett. 2012, 3, 3538). Here we computationally identify second-sphere amino acid residues predicted to influence the freedom of the catalytic site vibrational modes linked to heavy enzyme effects in PNP. We mutated heavy and light PNPs to increase the catalytic site vibrational freedom. Enzymatic barrier-crossing rates were converted from mass-dependent to mass-independent as a result of the mutations. The mutagenic uncoupling of femtosecond motions between catalytic site groups and reactants decreased transition state barrier crossing by 2 orders of magnitude, an indication of the femtosecond dynamic contributions to catalysis.

PubMed: 26927977
DOI: 10.1021/jacs.5b12551

Experimental method

X-RAY DIFFRACTION (2.3 Å)