5KSI

Crystal structure of deoxygenated hemoglobin in complex with sphingosine phosphate and 2,3-Bisphosphoglycerate

  • Classification: OXYGEN TRANSPORT
  • Organism(s): Homo sapiens

  • 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; National Institutes of Health/National Cancer Institute 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • 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 Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A, C
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, D
146Homo sapiensGene Names: HBB
Find proteins for P68871 (Homo sapiens)
Go to Gene View: HBB
Go to UniProtKB:  P68871
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DG2
Query on DG2

Download SDF File 
Download CCD File 
B, D
(2R)-2,3-diphosphoglyceric acid
2,3-Bisphosphoglyceric acid; 2,3-bisphosphoglycerate; 2,3-BPG; 2,3-diphosphoglyceric acid; 2,3-diphosphoglycerate; 2,3-DPG; (2~{R})-2,3-diphosphonooxypropanoic acid
C3 H8 O10 P2
XOHUEYCVLUUEJJ-UWTATZPHSA-N
 Ligand Interaction
HEM
Query on HEM

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.940α = 90.00
b = 98.080β = 90.00
c = 65.140γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
d*TREKdata reduction
d*TREKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute on Minority Health and Health DisparitiesUnited StatesMD009124
National Institutes of Health/National Cancer InstituteUnited StatesCA16059

Revision History 

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references