6MP5

Crystal structure of native human sulfide:quinone oxidoreductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

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.


    Related Citations: 
    • Human sulfide:quinone oxidoreductase catalyzes the first step in hydrogen sulfide metabolism and produces a sulfane sulfur metabolite.
      Jackson, M.R.,Melideo, S.L.,Jorns, M.S.
      (2012) Biochemistry 51: 6804
    • Role of human sulfide: quinone oxidoreductase in H2S metabolism.
      Jackson, M.R.,Melideo, S.L.,Jorns, M.S.
      (2015) Meth. Enzymol. 554: 255


    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
413Homo sapiensMutation(s): 0 
Gene Names: SQOR (SQRDL)
EC: 1.8.5.-
Find proteins for Q9Y6N5 (Homo sapiens)
Go to Gene View: SQOR
Go to UniProtKB:  Q9Y6N5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • 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
Aimlessdata scaling
PDB_EXTRACTdata extraction
DMphasing
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing

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