4L3V

Crystal structure of delta516-525 human cystathionine beta-synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.628 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 110: E3790-E3799

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

  • 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'-phosphat ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cystathionine beta-synthase
B, A, C
550Homo sapiensGene Names: CBS
EC: 4.2.1.22
Find proteins for P35520 (Homo sapiens)
Go to Gene View: CBS
Go to UniProtKB:  P35520
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B, C
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.628 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 227.750α = 90.00
b = 342.655β = 90.00
c = 107.253γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Database references
  • Version 1.2: 2013-10-16
    Type: Database references