Crystal structure of PtmU3 complexed with PTM substrate

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

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This is version 1.4 of the entry. See complete history


Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis.

Dong, L.B.Liu, Y.C.Cepeda, A.J.Kalkreuter, E.Deng, M.R.Rudolf, J.D.Chang, C.Joachimiak, A.Phillips Jr., G.N.Shen, B.

(2019) J Am Chem Soc 141: 12406-12412

  • DOI: https://doi.org/10.1021/jacs.9b06183
  • Primary Citation of Related Structures:  
    6OMP, 6OMQ, 6OMR

  • PubMed Abstract: 

    Nonheme diiron monooxygenases make up a rapidly growing family of oxygenases that are rarely identified in secondary metabolism. Herein, we report the in vivo, in vitro, and structural characterizations of a nonheme diiron monooxygenase, PtmU3, that installs a C-5 β-hydroxyl group in the unified biosynthesis of platensimycin and platencin, two highly functionalized diterpenoids that act as potent and selective inhibitors of bacterial and mammalian fatty acid synthases. This hydroxylation sets the stage for the subsequent A-ring cleavage step key to the unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 adopts an unprecedented triosephosphate isomerase (TIM) barrel structural fold for this class of enzymes and possesses a noncanonical diiron active site architecture with a saturated six-coordinate iron center lacking a μ-oxo bridge. This study reveals the first member of a previously unidentified superfamily of TIM-barrel-fold enzymes for metal-dependent dioxygen activation, with the majority predicted to act on CoA-linked substrates, thus expanding our knowledge of nature's repertoire of nonheme diiron monooxygenases and TIM-barrel-fold enzymes.

  • Organizational Affiliation

    Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
356Streptomyces platensisMutation(s): 0 
Find proteins for A0A0A0UVH9 (Streptomyces platensis)
Explore A0A0A0UVH9 
Go to UniProtKB:  A0A0A0UVH9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0UVH9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MZD

Download Ideal Coordinates CCD File 
O [auth B]S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,11alpha,13alpha)-7-hydroxy-11,16-epoxykaurane-18-thioate
C31 H51 N2 O10 P S
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
C2 H3 O2
Query on MN

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
P [auth B]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.564α = 90
b = 122.864β = 90
c = 139.936γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM114353

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description