5F74 | pdb_00005f74

Crystal structure of ChREBP:14-3-3 complex bound with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.188 (Depositor) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Metabolite Regulation of Nuclear Localization of Carbohydrate-response Element-binding Protein (ChREBP): ROLE OF AMP AS AN ALLOSTERIC INHIBITOR.

Sato, S.Jung, H.Nakagawa, T.Pawlosky, R.Takeshima, T.Lee, W.R.Sakiyama, H.Laxman, S.Wynn, R.M.Tu, B.P.MacMillan, J.B.De Brabander, J.K.Veech, R.L.Uyeda, K.

(2016) J Biological Chem 291: 10515-10527

  • DOI: https://doi.org/10.1074/jbc.M115.708982
  • Primary Citation Related Structures: 
    5F74

  • PubMed Abstract: 

    The carbohydrate-response element-binding protein (ChREBP) is a glucose-responsive transcription factor that plays an essential role in converting excess carbohydrate to fat storage in the liver. In response to glucose levels, ChREBP is regulated by nuclear/cytosol trafficking via interaction with 14-3-3 proteins, CRM-1 (exportin-1 or XPO-1), or importins. Nuclear localization of ChREBP was rapidly inhibited when incubated in branched-chain α-ketoacids, saturated and unsaturated fatty acids, or 5-aminoimidazole-4-carboxamide ribonucleotide. Here, we discovered that protein-free extracts of high fat-fed livers contained, in addition to ketone bodies, a new metabolite, identified as AMP, which specifically activates the interaction between ChREBP and 14-3-3. The crystal structure showed that AMP binds directly to the N terminus of ChREBP-α2 helix. Our results suggest that AMP inhibits the nuclear localization of ChREBP through an allosteric activation of ChREBP/14-3-3 interactions and not by activation of AMPK. AMP and ketone bodies together can therefore inhibit lipogenesis by restricting localization of ChREBP to the cytoplasm during periods of ketosis.


  • Organizational Affiliation
    • From the Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390.

Macromolecule Content 

  • Total Structure Weight: 51.12 kDa 
  • Atom Count: 2,095 
  • Modeled Residue Count: 249 
  • Deposited Residue Count: 442 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein beta/alpha246Mus musculusMutation(s): 0 
Gene Names: Ywhab
UniProt & NIH Common Fund Data Resources
Find proteins for Q9CQV8 (Mus musculus)
Explore Q9CQV8 
Go to UniProtKB:  Q9CQV8
IMPC:  MGI:1891917
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CQV8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbohydrate-responsive element-binding protein196Rattus norvegicusMutation(s): 0 
Gene Names: MlxiplWbscr14
UniProt
Find proteins for Q8VIP2 (Rattus norvegicus)
Explore Q8VIP2 
Go to UniProtKB:  Q8VIP2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VIP2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.255 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.188 (Depositor) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 42 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.62α = 90
b = 115.62β = 90
c = 59.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-03-30
    Changes: Database references
  • Version 1.2: 2016-06-01
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description