8ckp | pdb_00008ckp

X-ray structure of the crystallization-prone form of subfamily III haloalkane dehalogenase DhmeA from Haloferax mediterranei

spinqualitylabelsall models 8ckp, resolution 3.31Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8ckp is a 10 chain structure with sequence from Haloferax mediterranei. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3.31Å Ligands: CL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function I3R766_HALMT Publication Abstract from PubMed Haloalkane dehalogenase (HLD) enzymes employ an S(N) 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but a 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(DeltaGG) ) that provided diffraction-quality crystals. The 3.3 A crystal structure reveals that DhmeA(DeltaGG) forms a ring-like 20-mer structure with outer and inner diameter of ~200 A and ~80 A, 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. This article is protected by copyright. All rights reserved. Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and X-ray crystallography.,Chmelova K, Gao T, Polak M, Schenkmayerova A, Croll TI, Shaikh TR, Skarupova J, Chaloupkova R, Diederichs K, Read RJ, Damborsky J, Novacek J, Marek M Protein Sci. 2023 Aug 13:e4751. doi: 10.1002/pro.4751. PMID:37574754 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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