4PAN

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): Yes 

  • 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 (NIH/NEI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1074/jbc.M114.572875
  • Primary Citation of Related Structures:  
    4PAM, 4PAN, 4PAO, 4PAQ

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1354Rattus norvegicusMutation(s): 1 
Gene Names: Gnai1Gnai-1
UniProt
Find proteins for P10824 (Rattus norvegicus)
Explore P10824 
Go to UniProtKB:  P10824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10824
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.187 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.533α = 90
b = 121.533β = 90
c = 68.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesRO1 EY006062
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM095633
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM080403
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesRO1 MH090192
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesRO1 MH090192
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM099842
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesRO1 DK09737
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR026915
National Science Foundation (NSF, United States)United States0742762
National Science Foundation (NSF, United States)United States1305874

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references, Refinement description
  • Version 1.5: 2023-12-27
    Changes: Data collection