7WAS | pdb_00007was

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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.194 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7WAS

Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 85.99 kDa 
  • Atom Count: 6,104 
  • Modeled Residue Count: 726 
  • Deposited Residue Count: 752 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.194 (DCC) 
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

View Full Validation Report



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
  • Version 1.4: 2024-11-13
    Changes: Structure summary