4PAM

A conserved phenylalanine as relay between the 5 helix and the GDP binding region of heterotrimeric G protein

  • Classification: SIGNALING PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Escherichia coli
  • Mutation(s): 

  • Deposited: 2014-04-09 Released: 2014-07-30 
  • Deposition Author(s): Kaya, A.I., Lokits, A.D., Gilbert, J., Iverson, T.M., Meiler, J., Hamm, H.E.
  • Funding Organization(s): National Institutes of Health/National Eye Institute; National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Institute of Mental Health; National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Center for Research Resources; National Institutes of Science 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

A Conserved Phenylalanine as a Relay between the alpha 5 Helix and the GDP Binding Region of Heterotrimeric Gi Protein alpha Subunit.

Kaya, A.I.Lokits, A.D.Gilbert, J.A.Iverson, T.M.Meiler, J.Hamm, H.E.

(2014) J.Biol.Chem. 289: 24475-24487

  • DOI: 10.1074/jbc.M114.572875
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this acti ...

    G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process.


    Organizational Affiliation

    From the Departments of Pharmacology, Heidi.hamm@vanderbilt.edu.,From the Departments of Pharmacology, Biochemistry, and.,Neuroscience.,From the Departments of Pharmacology, Chemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232.,From the Departments of Pharmacology.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein G(i) subunit alpha-1
A
354Rattus norvegicusMutation(s): 1 
Gene Names: Gnai1 (Gnai-1)
Find proteins for P10824 (Rattus norvegicus)
Go to UniProtKB:  P10824
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SO3
Query on SO3

Download SDF File 
Download CCD File 
A
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.101 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.188 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 121.126α = 90.00
b = 121.126β = 90.00
c = 68.186γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye InstituteUnited StatesRO1 EY006062
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1 GM095633
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1 GM080403
National Institutes of Health/National Institute of Mental HealthUnited StatesRO1 MH090192
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1 GM099842
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesRO1 DK09737
National Institutes of Health/National Center for Research ResourcesUnited StatesS10 RR026915
National Institutes of ScienceUnited States0742762
National Institutes of ScienceUnited States1305874

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-06
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.4: 2017-11-22
    Type: Refinement description