6B3A | pdb_00006b3a

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

• PDB DOI: https://doi.org/10.2210/pdb6B3A/pdb

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


• 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 (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

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

• PubMed: 29096064 
• DOI: https://doi.org/10.1021/acschembio.7b00746
• Primary Citation of Related Structures:  
  6B39, 6B3A, 6B3B


• 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 A biosynthesis (AprA MT1). Fe ³⁺ -replete AprA MT1 catalyzes one or two methyl transfer reactions on the substrate malonyl-ACP (acyl carrier protein), whereas Co ²⁺ , Fe ²⁺ , Mn ²⁺ , and Ni ²⁺ 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 Mn ²⁺ , 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.

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Organizational Affiliation: 
• Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.
Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego , La Jolla, California 92093, United States.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States.
Department of Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
Department of Microbiology and Immunology, University of Michigan , Ann Arbor, Michigan 48109, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 75.37 kDa 
• Atom Count: 5,560 
• Modeled Residue Count: 631 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AprA Methyltransferase 1	A	652	Moorena bouillonii	Mutation(s): 2
UniProt
Find proteins for A0A1U7N2Z8 (Moorena bouillonii PNG) Explore A0A1U7N2Z8  Go to UniProtKB:  A0A1U7N2Z8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.519	α = 90
b = 87.05	β = 90
c = 135.961	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Skiba, M.A., Smith, J.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA108874
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008353

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description