5WQK

Crystal structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in complex with compound1

Summary for 5WQK

• Entry DOI: 10.2210/pdb5wqk/pdb
• Related: 5WQJ
• Descriptor: Sulfurtransferase, 4-methyl-2-(2-naphthalen-1-yl-2-oxidanylidene-ethyl)sulfanyl-1~{H}-pyrimidin-6-one, SODIUM ION, ... (4 entities in total)
• Functional Keywords: transferase-inhibitor complex, transferase/inhibitor
• Biological source: Mus musculus (Mouse)
• Total number of polymer chains: 2
• Total formula weight: 66105.94

Authors

Suwanai, Y.,Toma-Fukai, S.,Shimizu, T. (deposition date: 2016-11-27, release date: 2017-09-06, Last modification date: 2024-10-16)

Primary citation

Hanaoka, K.,Sasakura, K.,Suwanai, Y.,Toma-Fukai, S.,Shimamoto, K.,Takano, Y.,Shibuya, N.,Terai, T.,Komatsu, T.,Ueno, T.,Ogasawara, Y.,Tsuchiya, Y.,Watanabe, Y.,Kimura, H.,Wang, C.,Uchiyama, M.,Kojima, H.,Okabe, T.,Urano, Y.,Shimizu, T.,Nagano, T.
Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide
Sci Rep, 7:40227-40227, 2017

PubMed Abstract: Very recent studies indicate that sulfur atoms with oxidation state 0 or -1, called sulfane sulfurs, are the actual mediators of some physiological processes previously considered to be regulated by hydrogen sulfide (HS). 3-Mercaptopyruvate sulfurtransferase (3MST), one of three HS-producing enzymes, was also recently shown to produce sulfane sulfur (HS). Here, we report the discovery of several potent 3MST inhibitors by means of high-throughput screening (HTS) of a large chemical library (174,118 compounds) with our HS-selective fluorescent probe, HSip-1. Most of the identified inhibitors had similar aromatic ring-carbonyl-S-pyrimidone structures. Among them, compound 3 showed very high selectivity for 3MST over other HS/sulfane sulfur-producing enzymes and rhodanese. The X-ray crystal structures of 3MST complexes with two of the inhibitors revealed that their target is a persulfurated cysteine residue located in the active site of 3MST. Precise theoretical calculations indicated the presence of a strong long-range electrostatic interaction between the persulfur anion of the persulfurated cysteine residue and the positively charged carbonyl carbon of the pyrimidone moiety of the inhibitor. Our results also provide the experimental support for the idea that the 3MST-catalyzed reaction with 3-mercaptopyruvate proceeds via a ping-pong mechanism.

PubMed: 28079151
DOI: 10.1038/srep40227

Experimental method

X-RAY DIFFRACTION (1.7 Å)