7ZVD | pdb_00007zvd

K89 acetylated glucose-6-phosphate dehydrogenase (G6PD) in a complex with structural NADP+

• PDB DOI: https://doi.org/10.2210/pdb7ZVD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-15 Released: 2023-08-23 
• Deposition Author(s): Wu, F., Muskat, N.H., Nudelman, H., Shahar, A., Arbely, E.
• Funding Organization(s): European Research Council (ERC), Israel Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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

• PubMed: 37798264 
• DOI: https://doi.org/10.1038/s41467-023-41895-2
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Macromolecular Crystallography Research Center (MCRC), Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel.
Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. [e-mail].
Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. [e-mail].
The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 56.6 kDa 
• Atom Count: 4,026 
• Modeled Residue Count: 484 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A [auth N]	484	Homo sapiens	Mutation(s): 0  Gene Names: G6PD EC: 1.1.1.49 (PDB Primary Data), 1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11413 (Homo sapiens) Explore P11413  Go to UniProtKB:  P11413
PHAROS:  P11413 GTEx:  ENSG00000160211

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	B [auth N]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	A [auth N]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.289 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.22	α = 90
b = 172.22	β = 90
c = 216.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-23 
Deposition Author(s): Wu, F., Muskat, N.H., Nudelman, H., Shahar, A., Arbely, E.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	678461
Israel Science Foundation	Israel	1769/20

Revision History  

• 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
• Version 1.3: 2024-02-28
  Changes: Source and taxonomy
• Version 1.4: 2024-11-13
  Changes: Structure summary
• Version 1.5: 2026-03-04
  Changes: Refinement description