7VB8 | pdb_00007vb8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.189 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.180 (DCC) 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted STLClick on this verticalbar to view details

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 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-methyltransferaseA [auth B],
B [auth A]
377Sorghum 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 B],
O [auth A]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
STL (Subject of Investigation/LOI)
Query on STL

Download Ideal Coordinates CCD File 
C [auth B],
N [auth A]
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
K [auth B]
S [auth A]
V [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
E [auth B]
F [auth B]
G [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
U [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
EA [auth A],
L [auth B],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.189 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.180 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.831α = 90
b = 96.831β = 90
c = 168.038γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted STLClick on this verticalbar to view details

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: 2022-09-07
    Type: Initial release
  • Version 1.1: 2023-01-25
    Changes: Database references, Structure summary
  • Version 1.2: 2023-06-21
    Changes: Database references
  • Version 1.3: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary