7UCH

AprA Methyltransferase 1 - GNAT in complex with Mn2+ , SAM, and Di-methyl-malonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C -Methyltransferases.

Lao, Y.Skiba, M.A.Chun, S.W.Narayan, A.R.H.Smith, J.L.

(2022) ACS Chem Biol 17: 2088-2098

  • DOI: https://doi.org/10.1021/acschembio.2c00085
  • Primary Citation of Related Structures:  
    7UCH, 7UCI, 7UCL

  • PubMed Abstract: 

    Installation of methyl groups can significantly improve the binding of small-molecule drugs to protein targets; however, site-selective methylation often presents a significant synthetic challenge. Metal- and S -adenosyl-methionine (SAM)-dependent methyltransferases (MTs) in natural-product biosynthetic pathways are powerful enzymatic tools for selective or chemically challenging C-methylation reactions. Each of these MTs selectively catalyzes one or two methyl transfer reactions. Crystal structures and biochemical assays of the Mn 2+ -dependent monomethyltransferase from the saxitoxin biosynthetic pathway (SxtA MT) revealed the structural basis for control of methylation extent. The SxtA monomethyltransferase was converted to a dimethyltransferase by modification of the metal binding site, addition of an active site base, and an amino acid substitution to provide space in the substrate pocket for two methyl substituents. A reciprocal change converted a related dimethyltransferase into a monomethyltransferase, supporting our hypothesis that steric hindrance can prevent a second methylation event. A novel understanding of MTs will accelerate the development of MT-based catalysts and MT engineering for use in small-molecule synthesis.


  • Organizational Affiliation

    Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AprA Methyltransferase 1652Moorena bouilloniiMutation(s): 2 
UniProt
Find proteins for A0A1U7N2Z8 (Moorena bouillonii PNG)
Explore A0A1U7N2Z8 
Go to UniProtKB:  A0A1U7N2Z8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1U7N2Z8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.572α = 90
b = 88.283β = 90
c = 135.982γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesDK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA108874
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM008353
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM008270
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM067550

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description