Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis

Gerdes

Proc. Natl. Acad. Sci. U.S.A.

et al. 2015

153

252

It has been generally accepted that biosynthesis of protoheme (heme) uses a common set of core metabolic intermediates that includes protoporphyrin. Herein, we show that the Actinobacteria and Firmicutes (high-GC and low-GC Gram-positive bacteria) are unable to synthesize protoporphyrin. Instead, they oxidize coproporphyrinogen to coproporphyrin, insert ferrous iron to make Fe-coproporphyrin (coproheme), and then decarboxylate coproheme to generate protoheme. This pathway is specified by three genes named hemY, hemH, and hemQ. The analysis of 982 representative prokaryotic genomes is consistent with this pathway being the most ancient heme synthesis pathway in the Eubacteria. Our results identifying a previously unknown branch of tetrapyrrole synthesis support a significant shift from current models for the evolution of bacterial heme and chlorophyll synthesis. Because some organisms that possess this coproporphyrin-dependent branch are major causes of human disease, HemQ is a novel pharmacological target of significant therapeutic relevance, particularly given high rates of antimicrobial resistance among these pathogens.

Section: Resultsmentioning

confidence: 99%

Section: Identification Of the Terminal Enzymes Of Gram-positive Hemementioning

confidence: 99%

Noncanonical coproporphyrin-dependent bacterial heme biosynthesis pathway that does not use protoporphyrin

Gerdes

Proc. Natl. Acad. Sci. U.S.A.

et al. 2015

153

252

Proc. Natl. Acad. Sci. U.S.A.

“…To gain insight into the potential binding site of '882 within CgoX, the previously solved crystal structure of B. subtilis CgoX was interrogated (19) (Fig. 2D).…”

Section: Resultsmentioning

confidence: 99%

“…A flexible loop encompasses residues 183-186 that were identified in our initial mutational analysis. Importantly, previously published structures of CgoX are also incomplete in this region (19,20). Therefore, to further our understanding of the functional domain required for '882 activity in the absence of a crystal structure, the '882-CgoX interaction was modeled by in silico docking to identify additional residues that may be required for '882-induced activity of CgoX.…”

Section: In Silico Docking Identifies a Functional Domain Important Fmentioning

confidence: 99%

“…Taken together, these data begin to define a pocket within The two residues used to guide the docking are shown in cyan, whereas the two additional residues that were identified by the modeling approach and confirmed to have the desired disruption of '882 activity are shown in red. Structural analysis was performed on the B. subtilis crystal structure; homologous residue numbers to the S. aureus sequence are displayed (19). (B) CgoX activity was assayed with '882 and 5 μM CPGIII.…”

Section: In Silico Docking Identifies a Functional Domain Important Fmentioning

confidence: 99%

See 1 more Smart Citation

Antibacterial photosensitization through activation of coproporphyrinogen oxidase

Surdel

Horvath

Lojek

et al. 2017

Gram-positive bacteria cause the majority of skin and soft tissue infections (SSTIs), resulting in the most common reason for clinic visits in the United States. Recently, it was discovered that Gram-positive pathogens use a unique heme biosynthesis pathway, which implicates this pathway as a target for development of antibacterial therapies. We report here the identification of a small-molecule activator of coproporphyrinogen oxidase (CgoX) from Gram-positive bacteria, an enzyme essential for heme biosynthesis. Activation of CgoX induces accumulation of coproporphyrin III and leads to photosensitization of Gram-positive pathogens. In combination with light, CgoX activation reduces bacterial burden in murine models of SSTI. Thus, small-molecule activation of CgoX represents an effective strategy for the development of light-based antimicrobial therapies.

Molecular Simulations Bring New Insights into Protoporphyrinogen IX Oxidase/Protoporphyrinogen IX Interaction Modes

Wang

Wen

2016

Molecular Informatics

Self Cite

Protoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) catalyzes the oxidation of protoporphyrinogen IX (protogen IX) to protoporphyrin IX (proto IX) in the haem/chlorophyll biosynthetic pathway. Although extensive studies of PPO have already afforded many insights into its biological function and its significance to agriculture and medicine, details of the enzymatic mechanism as well as the nature of the specific amino acids involved in substrate binding still remain largely unknown due to the lack of structural information about protogen IX binding to PPO. In this study, we carried out a detailed and systematic investigation on the binding mode of protogen IX in the Nicotiana tabacum PPO (mtPPO) by performing a computational docking followed by molecular simulations, quantum mechanics calculations, and an integrated analysis. The proposed binding mode was consistent with experimental studies, and several potential key residues that have not been investigated in previous studies, such as Thr70, Arg233, Ser235, Ser474 and Lys477, were identified. In addition, we compared the binding modes of protogen IX in mtPPO and Homo sapiens PPO, and found their differences. Considering the low sequence identity and the differences of biochemical properties among the PPOs from various species, the investigation could provide a valuable basis for the design of PPO inhibitors with high potency and species-selectivity.