7LO2

S-adenosylmethionine synthetase cocrystallized with CTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases.

Gade, M.Tan, L.L.Damry, A.M.Sandhu, M.Brock, J.S.Delaney, A.Villar-Briones, A.Jackson, C.J.Laurino, P.

(2021) JACS Au 1: 2349-2360

  • DOI: https://doi.org/10.1021/jacsau.1c00464
  • Primary Citation of Related Structures:  
    7LL3, 7LNH, 7LNN, 7LO2, 7LOO, 7LOW, 7LOZ

  • PubMed Abstract: 

    Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.


  • Organizational Affiliation

    Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase
A, B, C, D
384Escherichia coli 908573Mutation(s): 0 
Gene Names: metKHMPREF1611_00479
EC: 2.5.1.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
KA [auth D]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
POP (Subject of Investigation/LOI)
Query on POP

Download Ideal Coordinates CCD File 
DA [auth C],
I [auth A],
OA [auth D],
V [auth B]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
MA [auth D],
NA [auth D],
S [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
W [auth B],
X [auth B],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
CA [auth C],
T [auth B],
U [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
LA [auth D],
R [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.139α = 90
b = 118.32β = 90
c = 144.456γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description