9PDH | pdb_00009pdh

X-ray structure of WT Drosophila Ahcy bound to NAD and adenosine at 2.50 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Drosophila Ahcy is a redox sensor that modulates gene expression to protect against light stress-induced retinal degeneration.

Stanhope, S.C.Singhal, K.Morato, N.M.Feng, Y.Meng, G.Marlin, M.N.Kotanko, C.C.Jarrett, M.M.Mesecar, A.D.Cooks, R.G.Weake, V.M.

(2025) Proc Natl Acad Sci U S A 122: e2511388122-e2511388122

  • DOI: https://doi.org/10.1073/pnas.2511388122
  • Primary Citation of Related Structures:  
    9PDH

  • PubMed Abstract: 

    One-carbon metabolism influences gene expression by providing methyl units for DNA, RNA, and histone methylation. Robust methylation requires rapid hydrolysis of the methylation by-product S -adenosylhomocysteine (SAH) by S -adenosylhomocysteinase (Ahcy). Ahcy is essential for maintaining methylation potential; however, the mechanisms governing its enzymatic activity, particularly in response to cellular stress, remain largely uncharacterized. Here, we show Ahcy is a redox-sensitive enzyme that is inhibited by oxidation of a conserved cysteine, C195, in vitro resulting in elevated SAH levels upon oxidative stress in vivo. We leveraged High-Throughput Desorption Electrospray Ionization Mass Spectrometry to directly quantify Ahcy enzymatic activity and observed that H 2 O 2 -induced oxidation significantly reduced its catalytic efficiency. Notably, while C195 is essential for enzymatic activity in Drosophila melanogaster and humans, this residue is not conserved in Caenorhabditis elegans Ahcy that is also insensitive to H 2 O 2 . Structural analysis revealed that C195 is positioned near NAD + in the active site, close to a second cysteine residue that is also lacking in C. elegans Ahcy. Ahcy oxidation is neuroprotective in a Drosophila light stress model that increases oxidative stress. Moreover, Ahcy knockdown suppresses light stress-induced gene expression changes in photoreceptors, although this response is uncoupled from changes in H3K4me3 and H3K27me3 levels, which were previously reported to alter in response to Ahcy knockdown in cultured cells. Thus, the one-carbon metabolism enzyme Ahcy senses changes in cellular redox homeostasis through a conserved cysteine residue that alters its activity, enabling rapid changes in gene expression that enable a neuroprotective response.


  • Organizational Affiliation
    • Department of Biochemistry, Purdue University, West Lafayette, IN 47907.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosylhomocysteinase
A, B, C, D
434Drosophila melanogasterMutation(s): 0 
Gene Names: AhcyAhcy13CG11654
EC: 3.13.2.1
UniProt
Find proteins for Q27580 (Drosophila melanogaster)
Explore Q27580 
Go to UniProtKB:  Q27580
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27580
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.315α = 90
b = 169.411β = 90
c = 127.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesR01EY033734

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Database references