Crystal structure of delta1-39 and delta516-525 human cystathionine beta-synthase D444N mutant containing C-terminal 6xHis tag

Experimental Data Snapshot

  • Resolution: 3.39 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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Structural basis of regulation and oligomerization of human cystathionine beta-synthase, the central enzyme of transsulfuration.

Ereno-Orbea, J.Majtan, T.Oyenarte, I.Kraus, J.P.Martinez-Cruz, L.A.

(2013) Proc Natl Acad Sci U S A 110: E3790-E3799

  • DOI: https://doi.org/10.1073/pnas.1313683110
  • Primary Citation of Related Structures:  
    4L0D, 4L27, 4L28, 4L3V

  • PubMed Abstract: 

    Cystathionine β-synthase (CBS) controls the flux of sulfur from methionine to cysteine, a precursor of glutathione, taurine, and H2S. CBS condenses serine and homocysteine to cystathionine with the help of three cofactors, heme, pyridoxal-5'-phosphate, and S-adenosyl-l-methionine. Inherited deficiency of CBS activity causes homocystinuria, the most frequent disorder of sulfur metabolism. We present the structure of the human enzyme, discuss the unique arrangement of the CBS domains in the C-terminal region, and propose how they interact with the catalytic core of the complementary subunit to regulate access to the catalytic site. This arrangement clearly contrasts with other proteins containing the CBS domain including the recent Drosophila melanogaster CBS structure. The absence of large conformational changes and the crystal structure of the partially activated pathogenic D444N mutant suggest that the rotation of CBS motifs and relaxation of loops delineating the entrance to the catalytic site represent the most likely molecular mechanism of CBS activation by S-adenosyl-l-methionine. Moreover, our data suggest how tetramers, the native quaternary structure of the mammalian CBS enzymes, are formed. Because of its central role in transsulfuration, redox status, and H2S biogenesis, CBS represents a very attractive therapeutic target. The availability of the structure will help us understand the pathogenicity of the numerous missense mutations causing inherited homocystinuria and will allow the rational design of compounds modulating CBS activity.

  • Organizational Affiliation

    Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), 48160 Bizkaia, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-synthaseA [auth B],
B [auth D],
C [auth A],
D [auth C]
548Homo sapiensMutation(s): 1 
Gene Names: CBS
UniProt & NIH Common Fund Data Resources
Find proteins for P35520 (Homo sapiens)
Explore P35520 
Go to UniProtKB:  P35520
PHAROS:  P35520
GTEx:  ENSG00000160200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35520
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.39 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.454α = 90
b = 190.454β = 90
c = 140.847γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2013-10-16
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description