5THY

Crystal structure of SeMet-Substituted CurJ carbon methyltransferase

  • Classification: TRANSFERASE,LYASE
  • Organism(s): Moorena producens 3L
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2016-09-30 Released: 2016-10-19 
  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Domain Organization and Active Site Architecture of a Polyketide Synthase C-methyltransferase.

Skiba, M.A.Sikkema, A.P.Fiers, W.D.Gerwick, W.H.Sherman, D.H.Aldrich, C.C.Smith, J.L.

(2016) ACS Chem Biol 11: 3319-3327

  • DOI: https://doi.org/10.1021/acschembio.6b00759
  • Primary Citation of Related Structures:  
    5THY, 5THZ

  • PubMed Abstract: 

    Polyketide metabolites produced by modular type I polyketide synthases (PKS) acquire their chemical diversity through the variety of catalytic domains within modules of the pathway. Methyltransferases are among the least characterized of the catalytic domains common to PKS systems. We determined the domain boundaries and characterized the activity of a PKS C-methyltransferase (C-MT) from the curacin A biosynthetic pathway. The C-MT catalyzes S-adenosylmethionine-dependent methyl transfer to the α-position of β-ketoacyl substrates linked to acyl carrier protein (ACP) or a small-molecule analog but does not act on β-hydroxyacyl substrates or malonyl-ACP. Key catalytic residues conserved in both bacterial and fungal PKS C-MTs were identified in a 2 Å crystal structure and validated biochemically. Analysis of the structure and the sequences bordering the C-MT provides insight into the positioning of this domain within complete PKS modules.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CurJ
A, B
405Moorena producens 3LMutation(s): 0 
Gene Names: LYNGBM3L_74460
UniProt
Find proteins for F4Y426 (Moorena producens 3L)
Explore F4Y426 
Go to UniProtKB:  F4Y426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF4Y426
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.35α = 90
b = 130.39β = 111.98
c = 62.83γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
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 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 StatesT32GM008353

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2016-12-28
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.4: 2017-10-11
    Changes: Data collection
  • Version 1.5: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.6: 2019-12-04
    Changes: Author supporting evidence