7RY4

Multi-conformer model of Ketosteroid Isomerase Y57F/D40N mutant from Pseudomonas Putida (pKSI) bound to a transition state analog at 250 K

Summary for 7RY4

• Entry DOI: 10.2210/pdb7ry4/pdb
• Related: 7RXF 7RXK
• Descriptor: Steroid Delta-isomerase, CHLORIDE ION, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: isomerase
• Biological source: Pseudomonas putida (Arthrobacter siderocapsulatus)
• Total number of polymer chains: 2
• Total formula weight: 29820.50

Authors

Yabukarski, F.,Doukov, T.,Herschlag, D. (deposition date: 2021-08-24, release date: 2022-11-09, Last modification date: 2023-11-22)

Primary citation

Yabukarski, F.,Doukov, T.,Pinney, M.M.,Biel, J.T.,Fraser, J.S.,Herschlag, D.
Ensemble-function relationships to dissect mechanisms of enzyme catalysis.
Sci Adv, 8:eabn7738-eabn7738, 2022

PubMed Abstract: Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (-effects) and changing the reactivity of each state (-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.

PubMed: 36240280
DOI: 10.1126/sciadv.abn7738

Experimental method

X-RAY DIFFRACTION (1.11 Å)