5DNI

Crystal structure of Methanocaldococcus jannaschii Fumarate hydratase beta subunit

Summary for 5DNI

• Entry DOI: 10.2210/pdb5dni/pdb
• Descriptor: Putative L(+)-tartrate dehydratase subunit beta, GLYCEROL, DI(HYDROXYETHYL)ETHER, ... (6 entities in total)
• Functional Keywords: alpha beta barrel, lyase
• Biological source: Methanocaldococcus jannaschii DSM 2661
• Total number of polymer chains: 2
• Total formula weight: 40738.49

Authors

Jayaraman, V.,Kunala, J.,Balaram, H. (deposition date: 2015-09-10, release date: 2016-09-14, Last modification date: 2023-11-29)

Primary citation

Bellur, A.,Das, S.,Jayaraman, V.,Behera, S.,Suryavanshi, A.,Balasubramanian, S.,Balaram, P.,Jindal, G.,Balaram, H.
Revisiting the Burden Borne by Fumarase: Enzymatic Hydration of an Olefin.
Biochemistry, 62:476-493, 2023

PubMed Abstract: Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, which have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon (Mj) as a model along with comparative analysis with the only other available class-I FH structure from (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large intersubunit rearrangements occur across apo- and holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis, and computational studies, including density functional theory (DFT) and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition-state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site.

PubMed: 36595439
DOI: 10.1021/acs.biochem.2c00541

Experimental method

X-RAY DIFFRACTION (2.3 Å)