5GM1

Crystal structure of methyltransferase TleD complexed with SAH


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 

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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

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-methylransferase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
297Streptomyces blastmyceticusMutation(s): 0 
Gene Names: tleD
UniProt
Find proteins for A0A077K7L1 (Streptomyces blastmyceticus)
Explore A0A077K7L1 
Go to UniProtKB:  A0A077K7L1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A077K7L1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
AA [auth H],
BA [auth I],
CA [auth J],
DA [auth K],
EA [auth L],
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
 Ligand Interaction
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 = 259.621α = 90
b = 152.902β = 93.33
c = 154.793γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science FoundationChina31570740

Revision History  (Full details and data files)

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