7WAS

SbSOMT in complex with pterostilbene and nicotinamide adenine dinucleotide(NAD+)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Regioselective stilbene O-methylations in Saccharinae grasses.

Lui, A.C.W.Pow, K.C.Lin, N.Lam, L.P.Y.Liu, G.Godwin, I.D.Fan, Z.Khoo, C.J.Tobimatsu, Y.Wang, L.Hao, Q.Lo, C.

(2023) Nat Commun 14: 3462-3462

  • DOI: https://doi.org/10.1038/s41467-023-38908-5
  • Primary Citation of Related Structures:  
    7VB8, 7WAQ, 7WAR, 7WAS

  • PubMed Abstract: 

    O-Methylated stilbenes are prominent nutraceuticals but rarely produced by crops. Here, the inherent ability of two Saccharinae grasses to produce regioselectively O-methylated stilbenes is reported. A stilbene O-methyltransferase, SbSOMT, is first shown to be indispensable for pathogen-inducible pterostilbene (3,5-bis-O-methylated) biosynthesis in sorghum (Sorghum bicolor). Phylogenetic analysis indicates the recruitment of genus-specific SOMTs from canonical caffeic acid O-methyltransferases (COMTs) after the divergence of Sorghum spp. from Saccharum spp. In recombinant enzyme assays, SbSOMT and COMTs regioselectively catalyze O-methylation of stilbene A-ring and B-ring respectively. Subsequently, SOMT-stilbene crystal structures are presented. Whilst SbSOMT shows global structural resemblance to SbCOMT, molecular characterizations illustrate two hydrophobic residues (Ile144/Phe337) crucial for substrate binding orientation leading to 3,5-bis-O-methylations in the A-ring. In contrast, the equivalent residues (Asn128/Asn323) in SbCOMT facilitate an opposite orientation that favors 3'-O-methylation in the B-ring. Consistently, a highly-conserved COMT is likely involved in isorhapontigenin (3'-O-methylated) formation in wounded wild sugarcane (Saccharum spontaneum). Altogether, our work reveals the potential of Saccharinae grasses as a source of O-methylated stilbenes, and rationalize the regioselectivity of SOMT activities for bioengineering of O-methylated stilbenes.


  • Organizational Affiliation

    School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
stilbene O-methyltransferase
A, B
376Sorghum bicolorMutation(s): 0 
Gene Names: SORBI_3007G059100
UniProt
Find proteins for A0A1B6PFV1 (Sorghum bicolor)
Explore A0A1B6PFV1 
Go to UniProtKB:  A0A1B6PFV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B6PFV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
3RL (Subject of Investigation/LOI)
Query on 3RL

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
Pterostilbene
C16 H16 O3
VLEUZFDZJKSGMX-ONEGZZNKSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
N [auth B]
Q [auth B]
E [auth A],
F [auth A],
K [auth B],
N [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
O [auth B],
P [auth B],
U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.469α = 90
b = 96.469β = 90
c = 169.43γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The University Grants Committee, Research Grants Council (RGC)Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references, Structure summary
  • Version 1.2: 2023-06-21
    Changes: Database references, Refinement description
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description