9H08 | pdb_00009h08

Crystal structure of Halide methyltransferase from Tulasnella calospora in complex with SAH at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Short-Circuiting the SAM-Cycle in Escherichia coli.

Li, Z.Wen, X.Bolotova, S.B.Seebeck, F.P.

(2025) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.5c17370
  • Primary Citation of Related Structures:  
    9H04, 9H05, 9H06, 9H07, 9H08, 9H09

  • PubMed Abstract: 

    Enzyme-mediated transfer of methyl groups to specific nucleophilic functions on small metabolites, proteins, and nucleic acids is an essential activity in all known life forms. Most of these transferred methyl groups originate from the one-carbon metabolism through methyl-tetrahydrofolate-dependent methylation of homocysteine, followed by adenosylation of methionine to form the primary methyltransferase cofactor, S -adenosylmethionine (SAM). In this report, we describe a strain of Escherichia coli with a Short-Circuited SAM-Cycle (SCSC) that maintains its SAM pool exclusively by methylating S -adenosylhomocysteine (SAH) using a synthetic methyl donor. Construction of this strain was made possible by the identification of an aryl sulfonate methyl ester as a biocompatible methyl donor and methyltransferases that accept this compound as substrate for in vivo methylation of SAH. We exploited this organism for the optimization of SAH-methylating enzymes by in vivo selection and to produce isotope-labeled natural products. Looking ahead, we anticipate that strains with SCSCs will open new possibilities for methyltransferase biocatalysis, natural product discovery, and bacterial metabolomics.


  • Organizational Affiliation
    • Department of Chemistry, University of Basel, Mattenstrasse 22, Basel 4002, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methyltransferase domain-containing protein252Tulasnella calospora MUT 4182Mutation(s): 0 
Gene Names: M407DRAFT_240870
UniProt
Find proteins for A0A0C3QM78 (Tulasnella calospora MUT 4182)
Explore A0A0C3QM78 
Go to UniProtKB:  A0A0C3QM78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0C3QM78
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
B [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.928α = 90
b = 59.928β = 90
c = 231.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2.multiplexdata scaling
PHASERphasing
xia2.multiplexdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss Nanoscience InstituteSwitzerlandP2104

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release