9O8U

(1-methylalkyl)succinate synthase alpha-beta-gamma-delta complex with bound fumarate

Summary for 9O8U

• Entry DOI: 10.2210/pdb9o8u/pdb
• EMDB information: 70238
• Descriptor: 1-methyl alkyl succinate synthase subunit MasD, MasB protein, 1-methyl alkyl succinate synthase subunit MasC, ... (8 entities in total)
• Functional Keywords: glycyl radical enzyme, (1-methylalkyl)succinate synthase, x-succinate synthase, alkylsuccinate synthase, hydrocarbon degradation, fumarate addition, lyase
• Biological source: Azoarcus sp. HxN1; More
• Total number of polymer chains: 6
• Total formula weight: 230769.97

Authors

Andorfer, M.C.,Drennan, C.L. (deposition date: 2025-04-16, release date: 2025-07-23, Last modification date: 2025-08-20)

Primary citation

Andorfer, M.C.,Levitz, T.S.,Liu, J.,Chakraborty, A.,King-Roberts, D.T.,Nweneka, D.,Imrich, C.N.,Drennan, C.L.
Structural basis for anaerobic alkane activation by a multisubunit glycyl radical enzyme.
Proc.Natl.Acad.Sci.USA, 122:e2510389122-e2510389122, 2025

PubMed Abstract: X-succinate synthases (XSSs) are glycyl radical enzymes (GREs) that catalyze the addition of hydrocarbons to fumarate via radical chemistry, thereby activating them for microbial metabolism. To date, the only structurally characterized XSS is benzylsuccinate synthase (BSS), which functionalizes toluene. A distinct subclass of XSSs acts on saturated hydrocarbons, which possess much stronger C(sp)-H bonds than toluene, suggesting mechanistic and structural differences from BSS. Here, we use cryogenic electron microscopy to determine the structure of one such enzyme, (1-methylalkyl)succinate synthase (MASS) from strain HxN1, which functionalizes -alkanes (C6-C8). The structure reveals an asymmetric dimer in which both sides contain a catalytic α-subunit and accessory γ-subunit. One α-subunit also binds two additional subunits, β and δ. The β-subunit binds a [4Fe-4S] cluster and adopts a fold similar to BSSβ. The β-subunit appears to regulate the flexibility of the α-subunit to enable opening of the active site, affording the binding of -alkane substrates. The δ-subunit, which lacks homology to known GRE subunits, adopts a rubredoxin-like fold that binds a single Fe ion, an architecture not previously reported for GREs. MASSδ occupies the same region of the α-subunit as the activating enzyme (AE) and may regulate the conformational changes required for glycyl radical installation. Structural comparisons between MASS and BSS reveal differences in how fumarate is bound and show amino acid substitutions that could account for the binding of alkanes versus toluene. Together, this structure offers insight into anaerobic alkane activation via fumarate addition.

PubMed: 40758891
DOI: 10.1073/pnas.2510389122

Experimental method

ELECTRON MICROSCOPY (2.8 Å)