5KSJ

Crystal structure of deoxygenated hemoglobin in complex with Sphingosine phosphate

  • Classification: OXYGEN TRANSPORT
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2016-07-08 Released: 2017-07-26 
  • Deposition Author(s): Ahmed, M.H., Safo, M.K., Xia, Y.
  • Funding Organization(s): National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural and Functional Insight of Sphingosine 1-Phosphate-Mediated Pathogenic Metabolic Reprogramming in Sickle Cell Disease.

Sun, K.D'Alessandro, A.Ahmed, M.H.Zhang, Y.Song, A.Ko, T.P.Nemkov, T.Reisz, J.A.Wu, H.Adebiyi, M.Peng, Z.Gong, J.Liu, H.Huang, A.Wen, Y.E.Wen, A.Q.Berka, V.Bogdanov, M.V.Abdulmalik, O.Han, L.Tsai, A.L.Idowu, M.Juneja, H.S.Kellems, R.E.Dowhan, W.Hansen, K.C.Safo, M.K.Xia, Y.

(2017) Sci Rep 7: 15281-15281

  • DOI: 10.1038/s41598-017-13667-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Elevated sphingosine 1-phosphate (S1P) is detrimental in Sickle Cell Disease (SCD), but the mechanistic basis remains obscure. Here, we report that increased erythrocyte S1P binds to deoxygenated sickle Hb (deoxyHbS), facilitates deoxyHbS anchoring t ...

    Elevated sphingosine 1-phosphate (S1P) is detrimental in Sickle Cell Disease (SCD), but the mechanistic basis remains obscure. Here, we report that increased erythrocyte S1P binds to deoxygenated sickle Hb (deoxyHbS), facilitates deoxyHbS anchoring to the membrane, induces release of membrane-bound glycolytic enzymes and in turn switches glucose flux towards glycolysis relative to the pentose phosphate pathway (PPP). Suppressed PPP causes compromised glutathione homeostasis and increased oxidative stress, while enhanced glycolysis induces production of 2,3-bisphosphoglycerate (2,3-BPG) and thus increases deoxyHbS polymerization, sickling, hemolysis and disease progression. Functional studies revealed that S1P and 2,3-BPG work synergistically to decrease both HbA and HbS oxygen binding affinity. The crystal structure at 1.9 Å resolution deciphered that S1P binds to the surface of 2,3-BPG-deoxyHbA and causes additional conformation changes to the T-state Hb. Phosphate moiety of the surface bound S1P engages in a highly positive region close to α1-heme while its aliphatic chain snakes along a shallow cavity making hydrophobic interactions in the "switch region", as well as with α2-heme like a molecular "sticky tape" with the last 3-4 carbon atoms sticking out into bulk solvent. Altogether, our findings provide functional and structural bases underlying S1P-mediated pathogenic metabolic reprogramming in SCD and novel therapeutic avenues.


    Organizational Affiliation

    Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China. yang.xia@uth.tmc.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alphaA, C141Homo sapiensMutation(s): 0 
Gene Names: HBA1HBA2
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
NIH Common Fund Data Resources
PHAROS  P69905
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit betaB, D146Homo sapiensMutation(s): 0 
Gene Names: HBB
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
NIH Common Fund Data Resources
PHAROS  P68871
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
S1P
Query on S1P

Download CCD File 
A
(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate
C18 H38 N O5 P
DUYSYHSSBDVJSM-KRWOKUGFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.18α = 90
b = 97.55β = 90
c = 65.03γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)United StatesMD009124
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA16059

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence