6VDZ
Crystal structure of reduced SfmD by soaking with sodium hydrosulfite
Summary for 6VDZ
| Entry DOI | 10.2210/pdb6vdz/pdb |
| Related | 6VDP 6VDQ |
| Descriptor | 3-methyl-L-tyrosine peroxygenase, HEME C (2 entities in total) |
| Functional Keywords | hydroxylase, histidine-ligated heme, oxidoreductase |
| Biological source | Streptomyces lavendulae |
| Total number of polymer chains | 1 |
| Total formula weight | 38851.40 |
| Authors | |
| Primary citation | Shin, I.,Davis, I.,Nieves-Merced, K.,Wang, Y.,McHardy, S.,Liu, A. A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis -His ligand set revealed by a de novo crystal structural and spectroscopic study. Chem Sci, 12:3984-3998, 2021 Cited by PubMed Abstract: SfmD is a heme-dependent enzyme in the biosynthetic pathway of saframycin A. Here, we present a 1.78 Å resolution crystal structure of SfmD, which unveils a novel heme cofactor attached to the protein with an unusual x xxx motif ( ∼ 38). This heme cofactor is unique in two respects. It contains a single thioether bond in a cysteine-vinyl link with Cys317, and the ferric heme has two axial protein ligands, , His274 and His313. We demonstrated that SfmD heme is catalytically active and can utilize dioxygen and ascorbate for a single-oxygen insertion into 3-methyl-l-tyrosine. Catalytic assays using ascorbate derivatives revealed the functional groups of ascorbate essential to its function as a cosubstrate. Abolishing the thioether linkage through mutation of Cys317 resulted in catalytically inactive SfmD variants. EPR and optical data revealed that the heme center undergoes a substantial conformational change with one axial histidine ligand dissociating from the iron ion in response to substrate 3-methyl-l-tyrosine binding or chemical reduction by a reducing agent, such as the cosubstrate ascorbate. The labile axial ligand was identified as His274 through redox-linked structural determinations. Together, identifying an unusual heme cofactor with a previously unknown heme-binding motif for a monooxygenase activity and the structural similarity of SfmD to the members of the heme-based tryptophan dioxygenase superfamily will broaden understanding of heme chemistry. PubMed: 34163669DOI: 10.1039/d0sc06369j PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.95 Å) |
Structure validation
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