Crystal structure of human cystathionine beta-synthase (delta516-525) in complex with AOAA.

Experimental Data Snapshot

  • Resolution: 2.69 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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H 2 S biogenesis by cystathionine beta-synthase: mechanism of inhibition by aminooxyacetic acid and unexpected role of serine.

Petrosino, M.Zuhra, K.Kopec, J.Hutchin, A.Szabo, C.Majtan, T.

(2022) Cell Mol Life Sci 79: 438-438

  • DOI: https://doi.org/10.1007/s00018-022-04479-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cystathionine beta-synthase (CBS) is a pivotal enzyme of the transsulfuration pathway responsible for diverting homocysteine to the biosynthesis of cysteine and production of hydrogen sulfide (H 2 S). Aberrant upregulation of CBS and overproduction of H 2 S contribute to pathophysiology of several diseases including cancer and Down syndrome. Therefore, pharmacological CBS inhibition has emerged as a prospective therapeutic approach. Here, we characterized binding and inhibitory mechanism of aminooxyacetic acid (AOAA), the most commonly used CBS inhibitor. We found that AOAA binds CBS tighter than its respective substrates and forms a dead-end PLP-bound intermediate featuring an oxime bond. Surprisingly, serine, but not cysteine, replaced AOAA from CBS and formed an aminoacrylate reaction intermediate, which allowed for the continuation of the catalytic cycle. Indeed, serine rescued and essentially normalized the enzymatic activity of AOAA-inhibited CBS. Cellular studies confirmed that AOAA decreased H 2 S production and bioenergetics, while additional serine rescued CBS activity, H 2 S production and mitochondrial function. The crystal structure of AOAA-bound human CBS showed a lack of hydrogen bonding with residues G305 and Y308, found in the serine-bound model. Thus, AOAA-inhibited CBS could be reactivated by serine. This difference may be important in a cellular environment in multiple pathophysiological conditions and may modulate the CBS-inhibitory activity of AOAA. In addition, our results demonstrate additional complexities of using AOAA as a CBS-specific inhibitor of H 2 S biogenesis and point to the urgent need to develop a potent, selective and specific pharmacological CBS inhibitor.

  • Organizational Affiliation

    Department of Pharmacology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musee 18, PER17, 1700, Fribourg, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-synthase
A, B
563Homo sapiensMutation(s): 0 
Gene Names: CBS
UniProt & NIH Common Fund Data Resources
Find proteins for P35520 (Homo sapiens)
Explore P35520 
Go to UniProtKB:  P35520
PHAROS:  P35520
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35520
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C34 H32 Fe N4 O4
IK2 (Subject of Investigation/LOI)
Query on IK2

Download Ideal Coordinates CCD File 
C10 H15 N2 O8 P
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.69 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.553α = 90
b = 134.573β = 90
c = 169.291γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release