6B3A

AprA Methyltransferase 1 - GNAT didomain in complex with Mn2+ and SAM

  • Classification: TRANSFERASE
  • Organism(s): Moorea bouillonii PNG
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2017-09-21 Released: 2017-11-15 
  • Deposition Author(s): Skiba, M.A., Smith, J.L.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease; National Institutes of Health/National Cancer Institute; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.784 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Mononuclear Iron-Dependent Methyltransferase Catalyzes Initial Steps in Assembly of the Apratoxin A Polyketide Starter Unit.

Skiba, M.A.Sikkema, A.P.Moss, N.A.Tran, C.L.Sturgis, R.M.Gerwick, L.Gerwick, W.H.Sherman, D.H.Smith, J.L.

(2017) ACS Chem. Biol. 12: 3039-3048

  • DOI: 10.1021/acschembio.7b00746
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Natural product biosynthetic pathways contain a plethora of enzymatic tools to carry out difficult biosynthetic transformations. Here, we discover an unusual mononuclear iron-dependent methyltransferase that acts in the initiation steps of apratoxin ...

    Natural product biosynthetic pathways contain a plethora of enzymatic tools to carry out difficult biosynthetic transformations. Here, we discover an unusual mononuclear iron-dependent methyltransferase that acts in the initiation steps of apratoxin A biosynthesis (AprA MT1). Fe3+-replete AprA MT1 catalyzes one or two methyl transfer reactions on the substrate malonyl-ACP (acyl carrier protein), whereas Co2+, Fe2+, Mn2+, and Ni2+ support only a single methyl transfer. MT1 homologues exist within the "GNAT" (GCN5-related N-acetyltransferase) loading modules of several modular biosynthetic pathways with propionyl, isobutyryl, or pivaloyl starter units. GNAT domains are thought to catalyze decarboxylation of malonyl-CoA and acetyl transfer to a carrier protein. In AprA, the GNAT domain lacks both decarboxylation and acyl transfer activity. A crystal structure of the AprA MT1-GNAT di-domain with bound Mn2+, malonate, and the methyl donor S-adenosylmethionine (SAM) reveals that the malonyl substrate is a bidentate metal ligand, indicating that the metal acts as a Lewis acid to promote methylation of the malonyl α-carbon. The GNAT domain is truncated relative to functional homologues. These results afford an expanded understanding of MT1-GNAT structure and activity and permit the functional annotation of homologous GNAT loading modules both with and without methyltransferases, additionally revealing their rapid evolutionary adaptation in different biosynthetic contexts.


    Organizational Affiliation

    Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AprA Methyltransferase 1
A
652Moorea bouillonii PNGMutation(s): 2 
Find proteins for A0A1U7N2Z8 (Moorea bouillonii PNG)
Go to UniProtKB:  A0A1U7N2Z8
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.784 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.519α = 90.00
b = 87.050β = 90.00
c = 135.961γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesDK042303
National Institutes of Health/National Cancer InstituteUnited StatesCA108874
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM008353

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references