8DSV

The structure of NicA2 in complex with N-methylmyosmine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Directed evolution unlocks oxygen reactivity for a nicotine-degrading flavoenzyme.

Dulchavsky, M.Mitra, R.Wu, K.Li, J.Boer, K.Liu, X.Zhang, Z.Vasquez, C.Clark, C.T.Funckes, K.Shankar, K.Bonnet-Zahedi, S.Siddiq, M.Sepulveda, Y.Suhandynata, R.T.Momper, J.D.Calabrese, A.N.George, O.Stull, F.Bardwell, J.C.A.

(2023) Nat Chem Biol 19: 1406-1414

  • DOI: https://doi.org/10.1038/s41589-023-01426-y
  • Primary Citation of Related Structures:  
    8DQ7, 8DQ8, 8DSV

  • PubMed Abstract: 

    The flavoenzyme nicotine oxidoreductase (NicA2) is a promising injectable treatment to aid in the cessation of smoking, a behavior responsible for one in ten deaths worldwide. NicA2 acts by degrading nicotine in the bloodstream before it reaches the brain. Clinical use of NicA2 is limited by its poor catalytic activity in the absence of its natural electron acceptor CycN. Without CycN, NicA2 is instead oxidized slowly by dioxygen (O 2 ), necessitating unfeasibly large doses in a therapeutic setting. Here, we report a genetic selection strategy that directly links CycN-independent activity of NicA2 to growth of Pseudomonas putida S16. This selection enabled us to evolve NicA2 variants with substantial improvement in their rate of oxidation by O 2 . The encoded mutations cluster around a putative O 2 tunnel, increasing flexibility and accessibility to O 2 in this region. These mutations further confer desirable clinical properties. A variant form of NicA2 is tenfold more effective than the wild type at degrading nicotine in the bloodstream of rats.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-dependent oxidoreductase
A, B
432Pseudomonas putidaMutation(s): 0 
Gene Names: A3L25_023855
EC: 1.4.2.2
UniProt
Find proteins for F8G0P2 (Pseudomonas putida (strain DSM 28022 / S16))
Explore F8G0P2 
Go to UniProtKB:  F8G0P2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8G0P2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA (Subject of Investigation/LOI)
Query on FDA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TXU (Subject of Investigation/LOI)
Query on TXU

Download Ideal Coordinates CCD File 
H [auth B]N-methylmyosmine
C10 H12 N2
TVKHGXPZBZKXFM-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.08α = 90
b = 86.7β = 90
c = 152.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Database references