Step 1: Understanding the Concept:
Molybdenum ($\text{Mo}$) is an essential transition metal cofactor in enzymes that catalyze key metabolic reactions in carbon, nitrogen, and sulfur cycles.
In almost all organisms, molybdenum must be bound to an organic scaffold to form a functional cofactor.
Step 2: Detailed Explanation:
There are two major classes of molybdenum-containing cofactors in nature:
1. Molybdenum-Molybdopterin Cofactor (Moco): In this cofactor, the molybdenum atom is coordinated to a tricyclic pyranopterin dithiolate ligand, known as molybdopterin.
The vast majority of molybdenum-dependent enzymes—including xanthine oxidase, nitrate reductase, and sulfite oxidase—utilize this Moco cofactor.
2. Iron-Molybdenum Cofactor (FeMoco): This is a complex metal cluster ($\text{Fe}_7\text{MoS}_9\text{C-homocitrate}$) that does not contain the molybdopterin organic ligand.
This unique FeMoco cluster is found exclusively in nitrogenase, the bacterial enzyme responsible for converting atmospheric nitrogen ($\text{N}_2$) into ammonia ($\text{NH}_3$) during biological nitrogen fixation.
Therefore, nitrogenase is the molybdenum-containing enzyme that does not contain molybdopterin as its cofactor.
Step 3: Final Answer:
The molybdenum-containing enzyme that does not contain molybdopterin is Nitrogenase, which corresponds to Option (D).