5TTK

Crystal Structure of Selenomethionine-incorporated Nicotine Oxidoreductase from Pseudomonas putida

• PDB DOI: https://doi.org/10.2210/pdb5TTK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida S16
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-11-03 Released: 2017-01-25 
• Deposition Author(s): Tararina, M.A., Janda, K.D., Allen, K.N.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Literature

Structural Analysis Provides Mechanistic Insight into Nicotine Oxidoreductase from Pseudomonas putida.

Tararina, M.A., Janda, K.D., Allen, K.N.

(2016) Biochemistry 55: 6595-6598

• PubMed: 27933790 
• DOI: https://doi.org/10.1021/acs.biochem.6b00963
• Primary Citation of Related Structures:  
  5TJR, 5TTJ, 5TTK


• PubMed Abstract: 
  

  The first structure of nicotine oxidoreductase (NicA2) was determined by X-ray crystallography. Pseudomonas putida has evolved nicotine-degrading activity to provide a source of carbon and nitrogen. The structure establishes NicA2 as a member of the monoamine oxidase family. Residues 1-50 are disordered and may play a role in localization. The nicotine-binding site proximal to the isoalloxazine ring of flavin shows an unusual composition of the classical aromatic cage (W427 and N462). The active site architecture is consistent with the proposed binding of the deprotonated form of the substrate and the flavin-dependent oxidation of the pyrrolidone C-N bond followed by nonenzymatic hydrolysis.

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Organizational Affiliation: 

Program in Biomolecular Pharmacology, Boston University School of Medicine , 72 East Concord Street, Boston, Massachusetts 02118, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 219.68 kDa 
• Atom Count: 13,917 
• Modelled Residue Count: 1,734 
• Deposited Residue Count: 1,960 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amine oxidase	A, B, C, D	490	Pseudomonas putida S16	Mutation(s): 0  Gene Names: PPS_4081 EC: 1.4.2.2
UniProt
Find proteins for F8G0P2 (Pseudomonas putida (strain DSM 28022 / S16)) Explore F8G0P2  Go to UniProtKB:  F8G0P2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 0.246 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.102	α = 90
b = 126.134	β = 90
c = 168.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Tararina, M.A., Janda, K.D., Allen, K.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	DA041839
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM008541

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Refinement description
• Version 1.2: 2019-12-11
  Changes: Advisory, Author supporting evidence, Derived calculations
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary