4COO

Crystal structure of human cystathionine beta-synthase (delta516-525) at 2.0 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inter-Domain Communication of Human Cystathionine Beta Synthase: Structural Basis of S-Adenosyl-L-Methionine Activation.

Mccorvie, T.J.Kopec, J.Hyung, S.Fitzpatrick, F.Feng, X.Termine, D.Strain-Damerell, C.Vollmar, M.Fleming, J.Janz, J.M.Bulawa, C.Yue, W.W.

(2014) J.Biol.Chem. 289: 36018

  • DOI: 10.1074/jbc.M114.610782
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cystathionine β-synthase (CBS) is a key enzyme in sulfur metabolism, and its inherited deficiency causes homocystinuria. Mammalian CBS is modulated by the binding of S-adenosyl-l-methionine (AdoMet) to its regulatory domain, which activates its catal ...

    Cystathionine β-synthase (CBS) is a key enzyme in sulfur metabolism, and its inherited deficiency causes homocystinuria. Mammalian CBS is modulated by the binding of S-adenosyl-l-methionine (AdoMet) to its regulatory domain, which activates its catalytic domain. To investigate the underlying mechanism, we performed x-ray crystallography, mutagenesis, and mass spectrometry (MS) on human CBS. The 1.7 Å structure of a AdoMet-bound CBS regulatory domain shows one AdoMet molecule per monomer, at the interface between two constituent modules (CBS-1, CBS-2). AdoMet binding is accompanied by a reorientation between the two modules, relative to the AdoMet-free basal state, to form interactions with AdoMet via residues verified by mutagenesis to be important for AdoMet binding (Phe(443), Asp(444), Gln(445), and Asp(538)) and for AdoMet-driven inter-domain communication (Phe(443), Asp(538)). The observed structural change is further supported by ion mobility MS, showing that as-purified CBS exists in two conformational populations, which converged to one in the presence of AdoMet. We therefore propose that AdoMet-induced conformational change alters the interface and arrangement between the catalytic and regulatory domains within the CBS oligomer, thereby increasing the accessibility of the enzyme active site for catalysis.


    Organizational Affiliation

    From the Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYSTATHIONINE BETA-SYNTHASE
A, B
563Homo sapiensMutation(s): 0 
Gene 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

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Download CCD File 
A
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

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A, B
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: 2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.264α = 90.00
b = 116.193β = 90.00
c = 167.990γ = 90.00
Software Package:
Software NamePurpose
XIAdata scaling
PHASERphasing
REFMACrefinement
XIAdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references
  • Version 1.2: 2015-01-14
    Type: Database references