3KPD

Crystal Structure of the CBS domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L-methionine.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Binding of S-Methyl-5'-Thioadenosine and S-Adenosyl-l-Methionine to Protein MJ0100 Triggers an Open-to-Closed Conformational Change in Its CBS Motif Pair.

Lucas, M.Encinar, J.A.Arribas, E.A.Oyenarte, I.Garcia, I.G.Kortazar, D.Fernandez, J.A.Mato, J.M.Martinez-Chantar, M.L.Martinez-Cruz, L.A.

(2010) J Mol Biol 396: 800-820

  • DOI: 10.1016/j.jmb.2009.12.012
  • Primary Citation of Related Structures:  
    3KPB, 3KPC, 3KPD

  • PubMed Abstract: 
  • Cystathionine beta-synthase (CBS) domains are small motifs that are present in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targe ...

    Cystathionine beta-synthase (CBS) domains are small motifs that are present in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targets for rational drug design. The protein MJ0100 from Methanocaldococcus jannaschii includes a DUF39 domain of so far unknown function and a CBS domain pair (Bateman domain) at its C-terminus. This work presents the crystallographic analysis of four different states of the CBS motif pair of MJ0100 in complex with different numbers of S-adenosyl-L-methionine (SAM) and S-methyl-5'-thioadenosine (MTA) ligands, providing evidence that ligand-induced conformational reorganization of Bateman domain dimers could be an important regulatory mechanism. These observations are in contrast to what is known from most of the other Bateman domain structures but are supported by recent studies on the magnesium transporter MgtE. Our structures represent the first example of a CBS domain protein complexed with SAM and/or MTA and might provide a structural basis for understanding the molecular mechanisms regulated by SAM upon binding to the C-terminal domain of human CBS, whose structure remains unknown.


    Organizational Affiliation

    Unidad de Biología Estructural, CIC bioGUNE, Parque Tecnológico de Bizkaia, Ed. 800, 48160-Derio, Bizkaia, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein MJ0100ABCD122Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: MJ0100
EC: 2.8.1.16
Find proteins for Q57564 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57564 
Go to UniProtKB:  Q57564
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download CCD File 
B, C
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
MTA
Query on MTA

Download CCD File 
A, C, D
5'-DEOXY-5'-METHYLTHIOADENOSINE
C11 H15 N5 O3 S
WUUGFSXJNOTRMR-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.671α = 90
b = 165.794β = 90
c = 122.997γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance