Computational Characterization of the Substrate-Binding Mode in Coproporphyrinogen III Oxidase

Abstract

Abstract:Oxygen-dependent coproporphyrinogen III oxidase catalyzes the sequential decarboxylation of the propionate substituents present on the A and B rings of coproporphyrinogen III in the heme biosynthetic pathway. Although extensive experimental investigation of this enzyme has already afforded many insights on its reaction mechanism, several key features (such as the substrate binding mode, the characterization of the active site and the initial substrate protonation state) remain poorly described. The molecular dynamics simulations described in this paper enabled the determination of a very promising substrate binding mode and the extensive characterization of the enzyme active site. The proposed binding mode is fully consistent with the known selectivity of the active site towards substituted tetrapyrroles, and explains the lack of activity of the H131A, R135A, D274A and R275A mutants and the reasons behind the non-occurrence of catalysis on the C and D rings of the tetrapyrrole.An important role in this binding mode is fulfilled by G276, as its carbonyl oxygen intervenes in the substrate anchoring by hydrogen-bonding its ring D pyrrole NH group. The presence of this interaction (which is only possible with protonated NH pyrrole group), and the absence of positively-charged side chains close to the pyrrole nitrogen (which might stabilize the N-deprotonated pyrrole postulated in some mechanistic proposals) shows that the pyrrole ring is very unlikely to undergo deprotonation during the catalytic cycle and allow the discrimination between the previously postulated mechanistic proposals.

Mitochondria and Iron: current questions

“…The enzyme involved in this step is coproporphyrinogen III oxidase (CPO), an oxygen-dependent enzyme located in the mitochondrial intermembrane space [61]. In the next step, six hydrogen atoms are removed from the porphyrinogen ring to form protoporphyrin IX.…”

One ring to rule them all: Trafficking of heme and heme synthesis intermediates in the metazoans

“…CPOX will utilize only the coproporphyrinogen III isomer and proceeds in a stepwise fashion that requires two molecules of molecular oxygen and generates two molecules of CO 2 . The reaction catalyzed by CPOX has been extensively studied both experimentally and in silico, but at present no definitive mechanism has been identified [40, 41]. …”

Computation-Aided Rational Deletion of C-Terminal Region Improved the Stability, Activity, and Expression Level of GH2 β-Glucuronidase

“…Although several strategies have been proposed on the basis of the B factor or sequence alignment, more efforts are still required to achieve rational design for identifying unstable loops. Recently, computational modeling methods such as molecular dynamics (MD) simulations have also been applied to assist in mutation design, − providing ideas and a theoretical basis to guide experiments. Therefore, it is anticipated that the combination of structural analysis and computation may be a promising pathway for the efficient design of mutants.…”