9N1D

Crystal structure of CysS from Corallococcus sp. CA054B with 5'-deoxyadenosine and methionine bound

Summary for 9N1D

• Entry DOI: 10.2210/pdb9n1d/pdb
• Descriptor: Radical SAM enzyme CysS, COBALAMIN, IRON/SULFUR CLUSTER, ... (7 entities in total)
• Functional Keywords: cystobactamids, radical s-adenosylmethionine methylase, cobalamin, oxidoreductase
• Biological source: Corallococcus sp. CA054B
• Total number of polymer chains: 1
• Total formula weight: 75291.87

Authors

Wang, B.,Cui, J.,Booker, S.J. (deposition date: 2025-01-25, release date: 2026-01-28)

Primary citation

Cui, J.,Wang, B.,Maurya, R.K.,Booker, S.J.
Structural basis for iterative methylation by a cobalamin-dependent radical S -adenosylmethionine enzyme in cystobactamids biosynthesis.
Proc.Natl.Acad.Sci.USA, 123:e2527019123-e2527019123, 2026

PubMed Abstract: Cystobactamids are nonribosomal peptide natural products that function as DNA gyrase inhibitors, exhibiting significant antibacterial activity. They are isolated from Cystobacter sp. Cbv34 and contain various alkoxy groups on para-aminobenzoic acid moieties, which are believed to play a crucial role in antibacterial functions. The alkoxy groups are generated by iterative methylations on a methoxy group by the cobalamin (Cbl)-dependent radical -adenosylmethionine (SAM) enzyme CysS. CysS catalyzes up to three methylations to give ethoxy, isopropoxy, sec-butoxy, and tert-butoxy groups. For each methylation, CysS uses a ping-pong mechanism in which two molecules of SAM are consumed. One SAM is used to methylate cob(I)alamin, while another generates a 5'-deoxyadenosyl 5'-radical to initiate substrate methylation. However, little is known about how the enzyme promotes both Cbl methylation and iterative substrate methylation, which occur by polar S2 and radical processes, respectively. Here, we report three X-ray crystal structures of a homolog of CysS from . Two were determined in the presence of methoxy- and ethoxy-containing substrates, showing how CysS accommodates substrates and products during iterative methylation. The third structure, determined in the absence of a substrate, exhibits structural changes that reorient the SAM's conformation to allow for the methylation of cob(I)alamin.

PubMed: 41564129
DOI: 10.1073/pnas.2527019123

Experimental method

X-RAY DIFFRACTION (1.94 Å)