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TitleMultimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography.
Journal, issue, pagesProtein Sci, Vol. 32, Issue 10, Page e4751, Year 2023
Publish dateSep 29, 2023
AuthorsKlaudia Chmelova / Tadeja Gao / Martin Polak / Andrea Schenkmayerova / Tristan I Croll / Tanvir R Shaikh / Jana Skarupova / Radka Chaloupkova / Kay Diederichs / Randy J Read / Jiri Damborsky / Jiri Novacek / Martin Marek /
PubMed AbstractHaloalkane dehalogenase (HLD) enzymes employ an S 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well- ...Haloalkane dehalogenase (HLD) enzymes employ an S 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but the mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and x-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeA ) that provided diffraction-quality crystals. The 3.3 Å crystal structure reveals that DhmeA forms a ring-like 20-mer structure with outer and inner diameter of ~200 and ~80 Å, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization, and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates.
External linksProtein Sci / PubMed:37574754 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.31 - 7.0 Å
Structure data

EMDB-16998: Cryo-EM structure of subfamily III haloalkane dehalogenase DhmeA from Haloferax mediterranei
Method: EM (single particle) / Resolution: 7.0 Å

17015

8ooh

EMDB-17015, PDB-8ooh:
Cryo-EM map of the focused refinement of the subfamily III haloalkane dehalogenase from Haloferax mediterranei dimer forming hexameric assembly.
Method: EM (single particle) / Resolution: 7.0 Å

PDB-8ckp:
X-ray structure of the crystallization-prone form of subfamily III haloalkane dehalogenase DhmeA from Haloferax mediterranei
Method: X-RAY DIFFRACTION / Resolution: 3.31 Å

Chemicals

ChemComp-CL:
Unknown entry / Chloride

ChemComp-HOH:
WATER / Water

Source
  • haloferax mediterranei (archaea)
KeywordsUNKNOWN FUNCTION / haloalkane dehalogenase-like / hydrolase / haloalkane dehalogenase

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