6MO6

Crystal structure of the selenomethionine-substituted human sulfide:quinone oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-Ray Structure of Human Sulfide:Quinone Oxidoreductase: Insights into the Mechanism of Mitochondrial Hydrogen Sulfide Oxidation.

Jackson, M.R.Loll, P.J.Jorns, M.S.

(2019) Structure 27: 794-805.e4

  • DOI: 10.1016/j.str.2019.03.002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Hydrogen sulfide (H <sub>2 </sub>S) is a gasotransmitter exhibiting pivotal functions in diverse biological processes, including activation of multiple cardioprotective pathways. Sulfide:quinone oxidoreductase (SQOR) is an integral membrane flavoprot ...

    Hydrogen sulfide (H 2 S) is a gasotransmitter exhibiting pivotal functions in diverse biological processes, including activation of multiple cardioprotective pathways. Sulfide:quinone oxidoreductase (SQOR) is an integral membrane flavoprotein that catalyzes the first step in the mitochondrial metabolism of H 2 S. As such, it plays a critical role in controlling physiological levels of the gasotransmitter and has attracted keen interest as a potential drug target. We report the crystal structure of human SQOR, unraveling the molecular basis for the enzyme's ability to catalyze sulfane sulfur transfer reactions with structurally diverse acceptors. We demonstrate that human SQOR contains unique features: an electropositive surface depression implicated as a binding site for sulfane sulfur acceptors and postulated to funnel negatively charged substrates to a hydrophilic H 2 S-oxidizing active site, which is connected to a hydrophobic internal tunnel that binds coenzyme Q. These findings support a proposed model for catalysis and open the door for structure-based drug design.


    Organizational Affiliation

    Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15(th) Street, Philadelphia, PA 19102, USA.,Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15(th) Street, Philadelphia, PA 19102, USA. Electronic address: mj27@drexel.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sulfide:quinone oxidoreductase, mitochondrial
A, B, C, D
414Homo sapiensMutation(s): 0 
Gene Names: SQOR (SQRDL)
EC: 1.8.5.-
Membrane protein
mpstruc
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Oxidoreductases (Monotopic)
Protein: 
Sulfide:quinone oxidoreductase, selenomethionine-substituted
Find proteins for Q9Y6N5 (Homo sapiens)
Go to Gene View: SQOR
Go to UniProtKB:  Q9Y6N5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.187 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 119.390α = 90.00
b = 119.390β = 90.00
c = 551.858γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
REFMACrefinement
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107389
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR41 HL134435

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-15
    Type: Data collection, Database references
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence