6ECU | pdb_00006ecu

SeMet substituted StiD O-MT residues 976-1266

• PDB DOI: https://doi.org/10.2210/pdb6ECU/pdb

• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.227 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

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

• PubMed: 30489068 
• DOI: https://doi.org/10.1021/acschembio.8b00687
• Primary Citation 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.

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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.
Department of Medicinal Chemistry , University of Minnesota , Minneapolis , Minnesota 55455 , United States.
Chemical Biology Doctoral Program , University of Michigan , Ann Arbor , Michigan 48109 , United States.
Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15206 , 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 72.32 kDa 
• Atom Count: 4,629 
• Modeled Residue Count: 554 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
StiD protein	A, B	316	Stigmatella aurantiaca	Mutation(s): 0  Gene Names: stiD
UniProt
Find proteins for Q8RJY3 (Stigmatella aurantiaca) Explore Q8RJY3  Go to UniProtKB:  Q8RJY3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.227 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.3	α = 89.6
b = 52.4	β = 88.3
c = 68.7	γ = 81.1

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Skiba, M.A., Bivins, M.M., 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: 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: 2024-10-23
  Changes: Data collection, Database references, Structure summary