7UF8

Structure of CtdP in complex with penicimutamide E and NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted N3LClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity.

Liu, Z.Rivera, S.Newmister, S.A.Sanders, J.N.Nie, Q.Liu, S.Zhao, F.Ferrara, J.D.Shih, H.W.Patil, S.Xu, W.Miller, M.D.Phillips, G.N.Houk, K.N.Sherman, D.H.Gao, X.

(2023) Nat Chem 15: 526-534

  • DOI: https://doi.org/10.1038/s41557-022-01117-6
  • Primary Citation of Related Structures:  
    7UF8

  • PubMed Abstract: 

    The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions. Here we report the discovery and characterization of CtdP, a member of a new class of bifunctional oxidoreductase/Diels-Alderase, which was previously annotated as an NmrA-like transcriptional regulator. We demonstrate that CtdP catalyses the inherently disfavoured cycloaddition to form the bicyclo[2.2.2]diazaoctane scaffold with a strict α-anti-selectivity. Guided by computational studies, we reveal a NADP + /NADPH-dependent redox mechanism for the CtdP-catalysed inverse electron demand Diels-Alder cycloaddition, which serves as the first example of a bifunctional Diels-Alderase that utilizes this mechanism.


  • Organizational Affiliation

    Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CtdP
A, B, C, D
348Penicillium citrinumMutation(s): 0 
Gene Names: ctdP
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
J [auth C],
L [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
N3L (Subject of Investigation/LOI)
Query on N3L

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth D]
Penicimutamide E
C21 H25 N3 O
LBTZXCFDJFHPMI-HBGVWJBISA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth B],
K [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.759α = 90
b = 166.759β = 90
c = 195.382γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata processing
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAPClick on this verticalbar to view detailsBest fitted N3LClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5 T32 GM 132046-2
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35 GM118101

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary