The first branching point in porphyrin biosynthesis : a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase

• In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

Subject headings

NATURVETENSKAP  -- Kemi -- Fysikalisk kemi (hsv//swe)

NATURAL SCIENCES  -- Chemical Sciences -- Physical Chemistry (hsv//eng)

NATURVETENSKAP  -- Kemi -- Teoretisk kemi (hsv//swe)

NATURAL SCIENCES  -- Chemical Sciences -- Theoretical Chemistry (hsv//eng)

Keyword

uroporphyrinogen decarboxylase III

uroporphyrinogen III

porphyrin biosynthesis

quantum mechanics/molecular mechanics and density functional theory

NATURAL SCIENCES

NATURVETENSKAP

Physical chemistry

Fysikalisk kemi

Biophysical chemistry

Biofysikalisk kemi

Theoretical chemistry

Teoretisk kemi

Quantum chemistry

Kvantkemi

Biochemistry

Biokemi

Publication and Content Type

ref (subject category)

art (subject category)