Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 598.12 kDa 
• Atom Count: 40182 
• Modelled Residue Count: 5045 
• Deposited Residue Count: 5346 
• Unique protein chains: 1

5GM1

Crystal structure of methyltransferase TleD complexed with SAH

• PDB DOI: 10.2210/pdb5GM1/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces blastmyceticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-12 Released: 2016-09-28 
• Deposition Author(s): Yu, F., Li, M.J., Xu, C.Y., Zhou, H., Sun, B., Wang, Z.J., Xu, Q., Xie, M.Y., Zuo, G., Huang, P., Wang, Q.S., He, J.H.
• Funding Organization(s): National Natural Science Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Literature

Crystal structure and enantioselectivity of terpene cyclization in SAM-dependent methyltransferase TleD

Yu, F., Li, M.J., Xu, C.Y., Sun, B., Zhou, H., Wang, Z.J., Xu, Q., Xie, M.Y., Zuo, G., Huang, P., Guo, H., Wang, Q.S., He, J.H.

(2016) Biochem J 473: 4385-4397

• PubMed: 27613858 
• DOI: 10.1042/BCJ20160695
• Primary Citation of Related Structures:  
  5GM1, 5GM2


• PubMed Abstract: 
  

TleD is a SAM (S-adenosyl-l-methionine)-dependent methyltransferase and acts as one of the key enzymes in the teleocidin B biosynthesis pathway. Besides methyl transferring, TleD also rearranges the geranyl and indole moieties of the precursor to form a six-membered ring. Moreover, it does not show homologies with any known terpenoid cyclases. In order to elucidate how such a remarkable reaction could be achieved, we determined the complex crystal structures of TleD and the cofactor analogue S-adenosyl-l-homocysteine with or without the substrate teleocidin A1. A domain-swapped pattern via an additional N-terminal α-helix is observed in TleD hexamers. Structural comparison and alignment shows that this additional N-terminal α-helix is the common feature of SAM methyltransferase-like cyclases TleD and SpnF. The residue Tyr ²¹ anchors the additional N-terminal α-helix to a 'core SAM-MT fold' and is a key residue for catalytic activity. Molecular dynamics simulation results suggest that the dihedral angle C23-C24-C25-C26 of teleocidin A1 is preferred to 60-90° in the TleD and substrate complex structure, which tend to adopt a Re-face stereocenter at C25 position after reaction and is according to in vitro enzyme reaction experiments. Our results also demonstrate that methyl transfer can be a new chemical strategy for carbocation formation in the terpene cyclization, which is the key initial step.

---

Organizational Affiliation: 

Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhang Heng Road, Pudong New District, Shanghai 201203, P.R. China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-methylransferase	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	297	Streptomyces blastmyceticus	Mutation(s): 0  Gene Names: tleD
UniProt
Find proteins for A0A077K7L1 (Streptomyces blastmyceticus) Explore A0A077K7L1  Go to UniProtKB:  A0A077K7L1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	AA [auth H], BA [auth I], CA [auth J], DA [auth K], EA [auth L], FA [auth M], GA [auth N], HA [auth O], IA [auth P], JA [auth Q], KA [auth R], S [auth A], T [auth B], U [auth B], V [auth C], W [auth D], X [auth E], Y [auth F], Z [auth G]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 259.621	α = 90
b = 152.902	β = 93.33
c = 154.793	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-07-12 
• Released Date: 2016-09-28 
Deposition Author(s): Yu, F., Li, M.J., Xu, C.Y., Zhou, H., Sun, B., Wang, Z.J., Xu, Q., Xie, M.Y., Zuo, G., Huang, P., Wang, Q.S., He, J.H.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation	China	31570740

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2016-12-07
  Changes: Database references