5WQJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

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Ligand Structure Quality Assessment 


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Literature

Discovery and Mechanistic Characterization of Selective Inhibitors of H2S-producing Enzyme: 3-Mercaptopyruvate Sulfurtransferase (3MST) Targeting Active-site Cysteine Persulfide

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.

(2017) Sci Rep 7: 40227-40227

  • DOI: https://doi.org/10.1038/srep40227
  • Primary Citation of Related Structures:  
    5WQJ, 5WQK

  • 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 (H 2 S). 3-Mercaptopyruvate sulfurtransferase (3MST), one of three H 2 S-producing enzymes, was also recently shown to produce sulfane sulfur (H 2 S n ). 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 H 2 S-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 H 2 S/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.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfurtransferase
A, B
297Mus musculusMutation(s): 3 
Gene Names: MpstmCG_13337
UniProt & NIH Common Fund Data Resources
Find proteins for Q99J99 (Mus musculus)
Explore Q99J99 
Go to UniProtKB:  Q99J99
IMPC:  MGI:2179733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99J99
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A, B
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Binding Affinity Annotations 
IDSourceBinding Affinity
7N3 Binding MOAD:  5WQJ Kd: 3000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.355α = 90
b = 150.36β = 110.09
c = 54.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release