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Title encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 121, Issue 21, Page e2400426121, Year 2024
Publish dateMay 21, 2024
AuthorsElif Eren / Norman R Watts / James F Conway / Paul T Wingfield /
PubMed AbstractEncapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic ...Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe to Fe for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.
External linksProc Natl Acad Sci U S A / PubMed:38748579 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.31 - 2.4 Å
Structure data

43290

8vjo

EMDB-43290, PDB-8vjo:
Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo
Method: EM (single particle) / Resolution: 2.4 Å

PDB-8vjn:
Myxococcus xanthus encapsulin cargo protein EncD in complex with flavin mononucleotide
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

Chemicals

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-HOH:
WATER

Source
  • myxococcus xanthus (bacteria)
KeywordsFLAVOPROTEIN / Encapsulin / cargo protein / EncD / flavin / flavin mononucleotide / EncA / VIRUS LIKE PARTICLE / iron / ferroxidase / ferritin / ferric reductase

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