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), 0.198 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.176 (DCC) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

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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: 86.55 kDa 
  • Atom Count: 6,638 
  • Modeled Residue Count: 726 
  • Deposited Residue Count: 754 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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]
CA [auth A],
DA [auth A],
K [auth B],
S [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [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]
AA [auth A],
BA [auth A],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
P [auth A],
Q [auth A],
R [auth A],
T [auth A],
Z [auth A]
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), 0.198 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.176 (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 


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