<i>Anabaena</i>sp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers

Yoshida, Toru; Ogola, Henry Joseph Oduor; Amano, Y.; Hisabori, Toru; Ashida, Hiroyuki; Sawa, Yousuke; Tsuge, Hideaki; Sugano, Yasushi

doi:10.1002/prot.24952

Cited by 15 publications

(17 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4D). The heme-binding pocket is essential to confer the catalytic activities of DyP (32). This active site is also involved in other residues, including Asp147, Arg238, Asn240, and Asp282, which are well conserved among the DyPs (SI Appendix, Fig.…”

Section: Resultsmentioning

confidence: 99%

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Tang

Zhang

et al. 2021

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

View full text Add to dashboard Cite

Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.

show abstract

Section: Resultsmentioning

confidence: 99%

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Tang

Zhang

et al. 2021

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

View full text Add to dashboard Cite

show abstract

“…The access to the internal cavity near the heme is limited by the radius of the tunnel gorge which is narrower in Cbo DyP (0.85 Å) compared to Tcu Dyp and DtpA (both 1.0 Å). This channel provides access of the hydrogen peroxide to the heme [13].…”

Section: Resultsmentioning

confidence: 99%

Characterization of a New DyP-Peroxidase from the Alkaliphilic Cellulomonad, Cellulomonas bogoriensis

2019

View full text Add to dashboard Cite

DyP-type peroxidases are heme-containing enzymes that have received increasing attention over recent years with regards to their potential as biocatalysts. A novel DyP-type peroxidase (CboDyP) was discovered from the alkaliphilic cellulomonad, Cellulomonas bogoriensis, which could be overexpressed in Escherichia coli. The biochemical characterization of the recombinant enzyme showed that it is a heme-containing enzyme capable to act as a peroxidase on several dyes. With the tested substrates, the enzyme is most active at acidic pH values and is quite tolerant towards solvents. The crystal structure of CboDyP was solved which revealed atomic details of the dimeric heme-containing enzyme. A peculiar feature of CboDyP is the presence of a glutamate in the active site which in most other DyPs is an aspartate, being part of the DyP-typifying sequence motif GXXDG. The E201D CboDyP mutant was prepared and analyzed which revealed that the mutant enzyme shows a significantly higher activity on several dyes when compared with the wild-type enzyme.

show abstract

“…A, tetramer) [53]. DAncDyPD-b1 and PosDyP4 have longer loops and are~50 residues larger than the latter four enzymes.…”

Section: Structural Characterizationmentioning

confidence: 96%

Mutational and structural analysis of an ancestral fungal dye‐decolorizing peroxidase

et al. 2021

View full text Add to dashboard Cite

Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process.

show abstract

Anabaenasp. DyP-type peroxidase is a tetramer consisting of two asymmetric dimers

Cited by 15 publications

References 36 publications

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Characterization of a New DyP-Peroxidase from the Alkaliphilic Cellulomonad, Cellulomonas bogoriensis

Mutational and structural analysis of an ancestral fungal dye‐decolorizing peroxidase

Contact Info

Product

Resources

About