7DMB | pdb_00007dmb

Crystal structure of trans-methyltransferase CalH complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb7DMB/pdb

• Classification: TRANSFERASE
• Organism(s): Aspergillus stellatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-03 Released: 2021-02-10 
• Deposition Author(s): Tao, H., Mori, T., Abe, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

One Polyketide Synthase, Two Distinct Products: Trans-Acting Enzyme-Controlled Product Divergence in Calbistrin Biosynthesis.

Tao, H., Mori, T., Wei, X., Matsuda, Y., Abe, I.

(2021) Angew Chem Int Ed Engl 60: 8851-8858

• PubMed: 33480463 
• DOI: https://doi.org/10.1002/anie.202016525
• Primary Citation Related Structures: 
  7DMB


• PubMed Abstract: 
  

  Calbistrins are fungal polyketides consisting of the characteristic decalin and polyene moieties. Although the biosynthetic gene cluster of calbistrin A was recently identified, the pathway of calbistrin A biosynthesis has largely remained uninvestigated. Herein, we investigated the mechanism by which the backbone structures of calbistrins are formed, by heterologous and in vitro reconstitution of the biosynthesis and a structural biological study. Intriguingly, our analyses revealed that the decalin and polyene portions of calbistrins are synthesized by the single polyketide synthase (PKS) CalA, with the aid of the trans-acting enoylreductase CalK and the trans-acting C-methyltransferase CalH, respectively. We also determined that the esterification of the two polyketide parts is catalyzed by the acyltransferase CalD. Our study has uncovered a novel dual-functional PKS and thus broadened our understanding of how fungi synthesize diverse polyketide natural products.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.
PRESTO (Japan) Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan.
Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.66 kDa 
• Atom Count: 6,255 
• Modeled Residue Count: 716 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative methyltransferase	A, B	386	Aspergillus stellatus	Mutation(s): 0
UniProt
Find proteins for A0A679DLY7 (Emericella variicolor) Explore A0A679DLY7  Go to UniProtKB:  A0A679DLY7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.81	α = 87.786
b = 60.594	β = 88.34
c = 71.146	γ = 89.742

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Tao, H., Mori, T., Abe, I.

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references