6OIB

Crystal structure of human Sulfide Quinone Oxidoreductase in complex with coenzyme Q

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-04-09 Released: 2020-01-15 
  • Deposition Author(s): Banerjee, R., Cho, U.S., Kim, H., Moon, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

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Literature

A Catalytic Trisulfide in Human Sulfide Quinone Oxidoreductase Catalyzes Coenzyme A Persulfide Synthesis and Inhibits Butyrate Oxidation.

Landry, A.P.Moon, S.Kim, H.Yadav, P.K.Guha, A.Cho, U.S.Banerjee, R.

(2019) Cell Chem Biol 26: 1515-1525.e4

  • DOI: https://doi.org/10.1016/j.chembiol.2019.09.010
  • Primary Citation of Related Structures:  
    6OI5, 6OI6, 6OIB, 6OIC

  • PubMed Abstract: 

    Mitochondrial sulfide quinone oxidoreductase (SQR) catalyzes the oxidation of H 2 S to glutathione persulfide with concomitant reduction of CoQ 10 . We report herein that the promiscuous activity of human SQR supported the conversion of CoA to CoA-SSH (CoA-persulfide), a potent inhibitor of butyryl-CoA dehydrogenase, and revealed a molecular link between sulfide and butyrate metabolism, which are known to interact. Three different CoQ 1 -bound crystal structures furnished insights into how diverse substrates access human SQR, and provided snapshots of the reaction coordinate. Unexpectedly, the active site cysteines in SQR are configured in a bridging trisulfide at the start and end of the catalytic cycle, and the presence of sulfane sulfur was confirmed biochemically. Importantly, our study leads to a mechanistic proposal for human SQR in which sulfide addition to the trisulfide cofactor eliminates 201 Cys-SSH, forming an intense charge-transfer complex with flavin adenine dinucleotide, and 379 Cys-SSH, which transfers sulfur to an external acceptor.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfide:quinone oxidoreductase, mitochondrial
A, B
418Homo sapiensMutation(s): 0 
Gene Names: SQORSQRDLCGI-44
EC: 1.8.5 (PDB Primary Data), 1.8.5.8 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6N5 (Homo sapiens)
Explore Q9Y6N5 
Go to UniProtKB:  Q9Y6N5
PHAROS:  Q9Y6N5
GTEx:  ENSG00000137767 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6N5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
H2S
Query on H2S

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
L [auth B]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.516α = 90
b = 111.512β = 90
c = 133.648γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM130183
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK111465

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release