5LWY

Revised crystal structure of the human adiponectin receptor 2 in complex with a C18 free fatty acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:3WXW


Literature

Structural insights into adiponectin receptors suggest ceramidase activity.

Vasiliauskaite-Brooks, I.Sounier, R.Rochaix, P.Bellot, G.Fortier, M.Hoh, F.De Colibus, L.Bechara, C.Saied, E.M.Arenz, C.Leyrat, C.Granier, S.

(2017) Nature 6: 120-123

  • DOI: 10.1038/nature21714
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty ...

    Adiponectin receptors (ADIPORs) are integral membrane proteins that control glucose and lipid metabolism by mediating, at least in part, a cellular ceramidase activity that catalyses the hydrolysis of ceramide to produce sphingosine and a free fatty acid (FFA). The crystal structures of the two receptor subtypes, ADIPOR1 and ADIPOR2, show a similar overall seven-transmembrane-domain architecture with large unoccupied cavities and a zinc binding site within the seven transmembrane domain. However, the molecular mechanisms by which ADIPORs function are not known. Here we describe the crystal structure of ADIPOR2 bound to a FFA molecule and show that ADIPOR2 possesses intrinsic basal ceramidase activity that is enhanced by adiponectin. We also identify a ceramide binding pose and propose a possible mechanism for the hydrolytic activity of ADIPOR2 using computational approaches. In molecular dynamics simulations, the side chains of residues coordinating the zinc rearrange quickly to promote the nucleophilic attack of a zinc-bound hydroxide ion onto the ceramide amide carbonyl. Furthermore, we present a revised ADIPOR1 crystal structure exhibiting a seven-transmembrane-domain architecture that is clearly distinct from that of ADIPOR2. In this structure, no FFA is observed and the ceramide binding pocket and putative zinc catalytic site are exposed to the inner membrane leaflet. ADIPOR1 also possesses intrinsic ceramidase activity, so we suspect that the two distinct structures may represent key steps in the enzymatic activity of ADIPORs. The ceramidase activity is low, however, and further studies will be required to characterize fully the enzymatic parameters and substrate specificity of ADIPORs. These insights into ADIPOR function will enable the structure-based design of potent modulators of these clinically relevant enzymes.


    Organizational Affiliation

    Institut de Génomique Fonctionnelle, CNRS UMR-5203 INSERM U1191, University of Montpellier, 34094 Montpellier, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V REGION HEAVY CHAINH119Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
V REGION LIGHT CHAINL107Mus musculusMutation(s): 0 
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adiponectin receptor protein 2A292Homo sapiensMutation(s): 0 
Gene Names: ADIPOR2PAQR2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Adiponectin Receptors
Protein: 
AdipoR1 adiponectin 1 receptor in complex with an Fv fragment
Find proteins for Q86V24 (Homo sapiens)
Explore Q86V24 
Go to UniProtKB:  Q86V24
NIH Common Fund Data Resources
PHAROS  Q86V24
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLB
Query on OLB

Download CCD File 
A
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-QJRAZLAKSA-N
 Ligand Interaction
OLA
Query on OLA

Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.58α = 90
b = 101.03β = 90
c = 108.63γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilFrance647687

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-04-12
    Changes: Database references
  • Version 1.3: 2017-04-19
    Changes: Atomic model, Structure summary
  • Version 1.4: 2018-02-07
    Changes: Advisory, Author supporting evidence, Database references
  • Version 1.5: 2018-12-05
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.6: 2019-10-16
    Changes: Data collection