5TJR

X-ray Crystal structure of a methylmalonate semialdehyde dehydrogenase from Pseudomonas sp. AAC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acs.biochem.6b00963
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylmalonate-semialdehyde dehydrogenase
A, B, C, D, E, F
531Pseudomonas sp. AACMutation(s): 0 
Find proteins for A0A081YAY7 (Pseudomonas sp. AAC)
Go to UniProtKB:  A0A081YAY7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.891α = 90.00
b = 156.631β = 90.00
c = 192.246γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-10-05 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Peat, T.S., Newman, J.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references