6NKK

Structure of PhqE Reductase/Diels-Alderase from Penicillium fellutanum in complex with NADP+ and premalbrancheamide

  • Classification: OXIDOREDUCTASE
  • Organism(s): Penicillium fellutanum
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-01-07 Released: 2019-10-09 
  • Deposition Author(s): Newmister, S.A., Dan, Q., Smith, J.L., Sherman, D.H.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.295 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase.

Dan, Q.Newmister, S.A.Klas, K.R.Fraley, A.E.McAfoos, T.J.Somoza, A.D.Sunderhaus, J.D.Ye, Y.Shende, V.V.Yu, F.Sanders, J.N.Brown, W.C.Zhao, L.Paton, R.S.Houk, K.N.Smith, J.L.Sherman, D.H.Williams, R.M.

(2019) Nat Chem 11: 972-980

  • DOI: https://doi.org/10.1038/s41557-019-0326-6
  • Primary Citation of Related Structures:  
    6NKH, 6NKI, 6NKK, 6NKM

  • PubMed Abstract: 

    Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide. Reductive cleavage of an L-Pro-L-Trp dipeptide from the MalG non-ribosomal peptide synthetase (NRPS) followed by reverse prenylation and a cascade of post-NRPS reactions culminates in an intramolecular [4+2] hetero-Diels-Alder (IMDA) cyclization to furnish the bicyclo[2.2.2]diazaoctane scaffold. Enzymatic assembly of optically pure (+)-premalbrancheamide involves an unexpected zwitterionic intermediate where MalC catalyses enantioselective cycloaddition as a bifunctional NADPH-dependent reductase/Diels-Alderase. The crystal structures of substrate and product complexes together with site-directed mutagenesis and molecular dynamics simulations demonstrate how MalC and PhqE (its homologue from the paraherquamide pathway) catalyse diastereo- and enantioselective cyclization in the construction of this important class of secondary metabolites.


  • Organizational Affiliation

    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short chain dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
265Penicillium fellutanumMutation(s): 0 
Gene Names: phqE
EC: 1.1
UniProt
Find proteins for L0E2Z4 (Penicillium fellutanum)
Explore L0E2Z4 
Go to UniProtKB:  L0E2Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0E2Z4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
PM7 (Subject of Investigation/LOI)
Query on PM7

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
(5aS,12aS,13aS)-12,12-dimethyl-2,3,11,12,12a,13-hexahydro-1H,5H,6H-5a,13a-(epiminomethano)indolizino[7,6-b]carbazol-14-one
C21 H25 N3 O
LBTZXCFDJFHPMI-DQLDELGASA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.336 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.295 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.586α = 90
b = 117.248β = 107.96
c = 64.809γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA070375
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM118101
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK042303

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-06
    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, Refinement description