6ECW

StiD O-MT residues 956-1266

  • Classification: TRANSFERASE
  • Organism(s): Stigmatella aurantiaca
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2018-08-08 Released: 2018-12-12 
  • Deposition Author(s): Skiba, M.A., Bivins, M.M., 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Polyketide Synthase O-Methylation.

Skiba, M.A.Bivins, M.M.Schultz, J.R.Bernard, S.M.Fiers, W.D.Dan, Q.Kulkarni, S.Wipf, P.Gerwick, W.H.Sherman, D.H.Aldrich, C.C.Smith, J.L.

(2018) ACS Chem Biol 13: 3221-3228

  • DOI: https://doi.org/10.1021/acschembio.8b00687
  • Primary Citation of Related Structures:  
    6ECT, 6ECU, 6ECV, 6ECW, 6ECX

  • PubMed Abstract: 

    Modular type I polyketide synthases (PKSs) produce some of the most chemically complex metabolites in nature through a series of multienzyme modules. Each module contains a variety of catalytic domains to selectively tailor the growing molecule. PKS O-methyltransferases ( O-MTs) are predicted to methylate β-hydroxyl or β-keto groups, but their activity and structure have not been reported. We determined the domain boundaries and characterized the catalytic activity and structure of the StiD and StiE O-MTs, which methylate opposite β-hydroxyl stereocenters in the myxobacterial stigmatellin biosynthetic pathway. Substrate stereospecificity was demonstrated for the StiD O-MT. Key catalytic residues were identified in the crystal structures and investigated in StiE O-MT via site-directed mutagenesis and further validated with the cyanobacterial CurL O-MT from the curacin biosynthetic pathway. Initial structural and biochemical analysis of PKS O-MTs supplies a new chemoenzymatic tool, with the unique ability to selectively modify hydroxyl groups during polyketide biosynthesis.


  • Organizational Affiliation

    Life Sciences Institute , 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
StiD protein
A, B
315Stigmatella aurantiacaMutation(s): 0 
Gene Names: stiD
UniProt
Find proteins for Q8RJY3 (Stigmatella aurantiaca)
Explore Q8RJY3 
Go to UniProtKB:  Q8RJY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RJY3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.086α = 90
b = 71.086β = 90
c = 123.036γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK042303
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA108874
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM008353

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references