7ZVE

K403 acetylated glucose-6-phosphate dehydrogenase (G6PD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Acetylation-dependent coupling between G6PD activity and apoptotic signaling.

Wu, F.Muskat, N.H.Dvilansky, I.Koren, O.Shahar, A.Gazit, R.Elia, N.Arbely, E.

(2023) Nat Commun 14: 6208-6208

  • DOI: https://doi.org/10.1038/s41467-023-41895-2
  • Primary Citation of Related Structures:  
    7ZVD, 7ZVE

  • PubMed Abstract: 

    Lysine acetylation has been discovered in thousands of non-histone human proteins, including most metabolic enzymes. Deciphering the functions of acetylation is key to understanding how metabolic cues mediate metabolic enzyme regulation and cellular signaling. Glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme in the pentose phosphate pathway, is acetylated on multiple lysine residues. Using site-specifically acetylated G6PD, we show that acetylation can activate (AcK89) and inhibit (AcK403) G6PD. Acetylation-dependent inactivation is explained by structural studies showing distortion of the dimeric structure and active site of G6PD. We provide evidence for acetylation-dependent K95/97 ubiquitylation of G6PD and Y503 phosphorylation, as well as interaction with p53 and induction of early apoptotic events. Notably, we found that the acetylation of a single lysine residue coordinates diverse acetylation-dependent processes. Our data provide an example of the complex roles of acetylation as a posttranslational modification that orchestrates the regulation of enzymatic activity, posttranslational modifications, and apoptotic signaling.


  • Organizational Affiliation

    Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase501Homo sapiensMutation(s): 0 
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
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UniProt GroupP11413
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase498Homo sapiensMutation(s): 0 
Gene Names: G6PD
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase497Homo sapiensMutation(s): 0 
Gene Names: G6PD
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase
D, H
499Homo sapiensMutation(s): 0 
Gene Names: G6PD
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
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Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase500Homo sapiensMutation(s): 0 
Gene Names: G6PD
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase497Homo sapiensMutation(s): 0 
Gene Names: G6PD
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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  • Reference Sequence
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenase496Homo sapiensMutation(s): 0 
EC: 1.1.1.49
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens)
Explore P11413 
Go to UniProtKB:  P11413
PHAROS:  P11413
GTEx:  ENSG00000160211 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11413
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth B],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
Q [auth J]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.363α = 77.23
b = 122.609β = 80.99
c = 161.31γ = 77.4
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union678461
Israel Science FoundationIsrael1769/20

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-02-07
    Changes: Database references