5UGH

Crystal structure of Mat2a bound to the allosteric inhibitor PF-02929366


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.062 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Targeting S-adenosylmethionine biosynthesis with a novel allosteric inhibitor of Mat2A.

Quinlan, C.L.Kaiser, S.E.Bolanos, B.Nowlin, D.Grantner, R.Karlicek-Bryant, S.Feng, J.L.Jenkinson, S.Freeman-Cook, K.Dann, S.G.Wang, X.Wells, P.A.Fantin, V.R.Stewart, A.E.Grant, S.K.

(2017) Nat. Chem. Biol. 13: 785-792

  • DOI: 10.1038/nchembio.2384

  • PubMed Abstract: 
  • S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Hu ...

    S-Adenosyl-L-methionine (SAM) is an enzyme cofactor used in methyl transfer reactions and polyamine biosynthesis. The biosynthesis of SAM from ATP and L-methionine is performed by the methionine adenosyltransferase enzyme family (Mat; EC 2.5.1.6). Human methionine adenosyltransferase 2A (Mat2A), the extrahepatic isoform, is often deregulated in cancer. We identified a Mat2A inhibitor, PF-9366, that binds an allosteric site on Mat2A that overlaps with the binding site for the Mat2A regulator, Mat2B. Studies exploiting PF-9366 suggested a general mode of Mat2A allosteric regulation. Allosteric binding of PF-9366 or Mat2B altered the Mat2A active site, resulting in increased substrate affinity and decreased enzyme turnover. These data support a model whereby Mat2B functions as an inhibitor of Mat2A activity when methionine or SAM levels are high, yet functions as an activator of Mat2A when methionine or SAM levels are low. The ramification of Mat2A activity modulation in cancer cells is also described.


    Organizational Affiliation

    Oncology Research and Development, Pfizer Inc., San Diego, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-adenosylmethionine synthase isoform type-2
A, B, C, D
397Homo sapiensMutation(s): 0 
Gene Names: MAT2A (AMS2, MATA2)
EC: 2.5.1.6
Find proteins for P31153 (Homo sapiens)
Go to Gene View: MAT2A
Go to UniProtKB:  P31153
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8AJ
Query on 8AJ

Download SDF File 
Download CCD File 
A, B, C
2-(7-chloro-5-phenyl[1,2,4]triazolo[4,3-a]quinolin-1-yl)-N,N-dimethylethan-1-amine
PF-02929366
C20 H19 Cl N4
LYLASWLQCMKZAT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
8AJIC50: 420000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.062 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.731α = 90.00
b = 109.100β = 100.04
c = 149.012γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Database references
  • Version 2.0: 2017-07-12
    Type: Non-polymer description, Structure summary