5UCU

STRUCTURAL AND MECHANISTIC INSIGHTS INTO HEMOGLOBIN-CATALYZED HYDROGEN SULFIDE OXIDATION AND THE FATE OF POLYSULFIDE PRODUCTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Mechanistic Insights into Hemoglobin-catalyzed Hydrogen Sulfide Oxidation and the Fate of Polysulfide Products.

Vitvitsky, V.Yadav, P.K.An, S.Seravalli, J.Cho, U.S.Banerjee, R.

(2017) J. Biol. Chem. 292: 5584-5592

  • DOI: 10.1074/jbc.M117.774943

  • PubMed Abstract: 
  • Hydrogen sulfide is a cardioprotective signaling molecule but is toxic at elevated concentrations. Red blood cells can synthesize H2S but, lacking organelles, cannot dispose of H2S via the mitochondrial sulfide oxidation pathway. We have recently sho ...

    Hydrogen sulfide is a cardioprotective signaling molecule but is toxic at elevated concentrations. Red blood cells can synthesize H2S but, lacking organelles, cannot dispose of H2S via the mitochondrial sulfide oxidation pathway. We have recently shown that at high sulfide concentrations, ferric hemoglobin oxidizes H2S to a mixture of thiosulfate and iron-bound polysulfides in which the latter species predominates. Here, we report the crystal structure of human hemoglobin containing low spin ferric sulfide, the first intermediate in heme-catalyzed sulfide oxidation. The structure provides molecular insights into why sulfide is susceptible to oxidation in human hemoglobin but is stabilized against it in HbI, a specialized sulfide-carrying hemoglobin from a mollusk adapted to life in a sulfide-rich environment. We have also captured a second sulfide bound at a postulated ligand entry/exit site in the α-subunit of hemoglobin, which, to the best of our knowledge, represents the first direct evidence for this site being used to access the heme iron. Hydrodisulfide, a postulated intermediate at the junction between thiosulfate and polysulfide formation, coordinates ferric hemoglobin and, in the presence of air, generated thiosulfate. At low sulfide/heme iron ratios, the product distribution between thiosulfate and iron-bound polysulfides was approximately equal. The iron-bound polysulfides were unstable at physiological glutathione concentrations and were reduced with concomitant formation of glutathione persulfide, glutathione disulfide, and H2S. Hence, although polysulfides are unlikely to be stable in the reducing intracellular milieu, glutathione persulfide could serve as a persulfide donor for protein persulfidation, a posttranslational modification by which H2S is postulated to signal.


    Organizational Affiliation

    From the Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Homo sapiensGene Names: HBA1, HBA2
Find proteins for P69905 (Homo sapiens)
Go to Gene View: HBA1 HBA2
Go to UniProtKB:  P69905
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta
B
146Homo sapiensGene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H2S
Query on H2S

Download SDF File 
Download CCD File 
A, B
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.797 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.186 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.766α = 90.00
b = 53.766β = 90.00
c = 193.254γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
xia2data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM112455
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK111465

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Refinement description