6VDP

Crystal structure of SfmD truncated variant

Summary for 6VDP

• Entry DOI: 10.2210/pdb6vdp/pdb
• Descriptor: 3-methyl-L-tyrosine peroxygenase, HEME C (3 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

Shin, I.,Liu, A. (deposition date: 2019-12-27, release date: 2021-03-10, Last modification date: 2024-10-23)

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

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: 34163669
DOI: 10.1039/d0sc06369j

Experimental method

X-RAY DIFFRACTION (2 Å)