4L27

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
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
EC: 4.2.1.22
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
F [auth B],
H [auth D],
J [auth A],
L [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth B],
G [auth D],
I [auth A],
K [auth C]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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