8IQ1

Crystal structure of hydrogen sulfide-bound superoxide dismutase in reduced state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Hydrogen sulfide functions as a micro-modulator bound at the copper active site of Cu/Zn-SOD to regulate the catalytic activity of the enzyme.

Wu, D.D.Jin, S.Cheng, R.X.Cai, W.J.Xue, W.L.Zhang, Q.Q.Yang, L.J.Zhu, Q.Li, M.Y.Lin, G.Wang, Y.Z.Mu, X.P.Wang, Y.Zhang, I.Y.Zhang, Q.Chen, Y.Cai, S.Y.Tan, B.Li, Y.Chen, Y.Q.Zhang, P.J.Sun, C.Yin, Y.Wang, M.J.Zhu, Y.Z.Tao, B.B.Zhou, J.H.Huang, W.X.Zhu, Y.C.

(2023) Cell Rep 42: 112750-112750

  • DOI: https://doi.org/10.1016/j.celrep.2023.112750
  • Primary Citation of Related Structures:  
    8IQ0, 8IQ1

  • PubMed Abstract: 

    The present study examines whether there is a mechanism beyond the current concept of post-translational modifications to regulate the function of a protein. A small gas molecule, hydrogen sulfide (H 2 S), was found to bind at active-site copper of Cu/Zn-SOD using a series of methods including radiolabeled binding assay, X-ray absorption near-edge structure (XANES), and crystallography. Such an H 2 S binding enhanced the electrostatic forces to guide the negatively charged substrate superoxide radicals to the catalytic copper ion, changed the geometry and energy of the frontier molecular orbitals of the active site, and subsequently facilitated the transfer of an electron from the superoxide radical to the catalytic copper ion and the breakage of the copper-His61 bridge. The physiological relevance of such an H 2 S effect was also examined in both in vitro and in vivo models where the cardioprotective effects of H 2 S were dependent on Cu/Zn-SOD.


  • Organizational Affiliation

    Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University Shanghai Medical College, Shanghai 200032, China; School of Stomatology, Henan University, Kaifeng, Henan 475004, China; Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]
A, B, C, D, E
A, B, C, D, E, F, G, H
151Bos taurusMutation(s): 0 
EC: 1.15.1.1
UniProt
Find proteins for P00442 (Bos taurus)
Explore P00442 
Go to UniProtKB:  P00442
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00442
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
KA [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D]
GA [auth E]
J [auth A]
M [auth B]
MA [auth F]
BA [auth D],
GA [auth E],
J [auth A],
M [auth B],
MA [auth F],
SA [auth G],
V [auth C],
WA [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth D]
FA [auth E]
I [auth A]
L [auth B]
LA [auth F]
AA [auth D],
FA [auth E],
I [auth A],
L [auth B],
LA [auth F],
RA [auth G],
U [auth C],
VA [auth H]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth H]
CA [auth D]
K [auth A]
NA [auth F]
O [auth B]
AB [auth H],
CA [auth D],
K [auth A],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
QA [auth F],
R [auth B],
UA [auth G],
W [auth C],
X [auth C],
XA [auth H],
Y [auth C],
YA [auth H],
ZA [auth H]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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BB [auth H]
CB [auth H]
EA [auth D]
IA [auth E]
JA [auth E]
BB [auth H],
CB [auth H],
EA [auth D],
IA [auth E],
JA [auth E],
T [auth B],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
H2S (Subject of Investigation/LOI)
Query on H2S

Download Ideal Coordinates CCD File 
HA [auth E],
N [auth B],
TA [auth G]
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.126α = 98.69
b = 69.961β = 94.83
c = 91.345γ = 103.31
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071446

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release