Crystal Structure of the MetH Reactivation Domain bound to Sinefungin

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.

Fick, R.J.Clay, M.C.Vander Lee, L.Scheiner, S.Al-Hashimi, H.Trievel, R.C.

(2018) Biochemistry 57: 3733-3740

  • DOI: https://doi.org/10.1021/acs.biochem.8b00375
  • Primary Citation of Related Structures:  
    6BDY, 6BM5, 6BM6

  • PubMed Abstract: 

    The C-terminal domain of cobalamin-dependent methionine synthase (MetH) has an essential role in catalyzing the reactivation of the enzyme following the oxidation of its cobalamin cofactor. This reactivation occurs through reductive methylation of the cobalamin using S-adenosylmethionine (AdoMet) as the methyl donor. Herein, we examine the molecular recognition of AdoMet by the MetH reactivation domain utilizing structural, biochemical, and computational approaches. Crystal structures of the Escherichia coli MetH reactivation domain in complex with AdoMet, the methyl transfer product S-adenosylhomocysteine (AdoHcy), and the AdoMet analogue inhibitor sinefungin illustrate that the ligands exhibit an analogous conformation within the solvent-exposed substrate binding cleft of the enzyme. AdoMet binding is stabilized by an intramolecular sulfur-oxygen chalcogen bond between the sulfonium and carboxylate groups of the substrate and by water-mediated carbon-oxygen hydrogen bonding between the sulfonium cation and the side chains of Glu1097 and Glu1128 that bracket the substrate binding cleft. AdoMet and sinefungin exhibited similar binding affinities for the MetH reactivation domain, whereas AdoHcy displayed an affinity for the enzyme that was an order of magnitude lower. Mutations of Glu1097 and Glu1128 diminished the AdoMet/AdoHcy binding selectivity ratio to approximately 2-fold, underscoring the role of these residues in enabling the enzyme to discriminate between the substrate and product. Together, these findings indicate that Glu1097 and Glu1128 in MetH promote high-affinity recognition of AdoMet and that sinefungin and potentially other AdoMet-based methyltransferase inhibitors can abrogate MetH reactivation, which would result in off-target effects associated with alterations in methionine homeostasis and one-carbon metabolism.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine synthase333Escherichia coli K-12Mutation(s): 0 
Gene Names: metHb4019JW3979
Find proteins for P13009 (Escherichia coli (strain K12))
Explore P13009 
Go to UniProtKB:  P13009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13009
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SFG

Download Ideal Coordinates CCD File 
C15 H23 N7 O5
Binding Affinity Annotations 
IDSourceBinding Affinity
SFG Binding MOAD:  6BDY Kd: 2040 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.35α = 90
b = 61.577β = 90
c = 139.877γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1508492

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-05-30
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description