6IZH

Crystal structure of deaminase AmnE from Pseudomonas sp. AP-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A Unique Homo-Hexameric Structure of 2-Aminomuconate Deaminase in the BacteriumPseudomonas species AP-3.

Chen, Y.Chen, Y.Jiang, H.Lu, D.Hu, T.Bi, G.Ran, Y.Yu, B.Dong, H.Su, D.

(2019) Front Microbiol 10: 2079-2079

  • DOI: https://doi.org/10.3389/fmicb.2019.02079
  • Primary Citation of Related Structures:  
    6IZH

  • PubMed Abstract: 

    The bacterium Pseudomonas species sp. AP-3 is one of several microorganisms that are capable of using 2-aminophenol as its sole source of carbon, nitrogen and energy. Several 2-aminophenol-metabolizing enzymes have pivotal roles in the biodegradation of aniline and its derivatives as environmental pollutants in Pseudomonas . The bacterium Pseudomonas sp. AP-3 recruits a unique 2-aminomuconate deaminase (AmnE) to hydrolyze 2-aminomuconate to 4-oxalocrotonate, and releases ammonia in the modified meta-cleavage pathway by forming various compounds-including acetaldehyde, pyruvic acid, acetyl-CoA, and succinate-that may enter the Krebs cycle. AmnE also belongs to the YjgF/YER057c/UK114 family (also known as the Rid family), which is conserved in all domains of life and prefers structurally homotrimeric forms with diverse functional purposes. To study the mechanism of the modified meta-cleavage pathway in Pseudomonas sp. AP-3 , we determined the first crystal structure of AmnE from Pseudomonas sp. AP-3 at 1.75 Å. AmnE forms a unique homohexamer instead of a trimer which is normally adopted by the members of YjgF/YER057c/UK114 family. Based on the structure of the AmnE hexamer, we observed a hydrophobic base composed of six Lp3 loops (residues 122-131) in each of the AmnE protomers that have pivotal roles in the assembly of the hexamer. Eighteen hydrogen bonds formed by the residues Met 96 , Pro 126 , and Arg 56 , which surround the hydrophobic base, allowed the combination of the two trimers into a stable hexamer. The single mutant of AmnE R56A lost the ability to maintain the hexameric conformation, and revealed that the hydrogen bonds between residues Arg 56 and Met 96 have pivotal roles in the AmnE hexameric assembly.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-aminomuconate deaminase
A, B, C, D, E
A, B, C, D, E, F, G, H, I
142Pseudomonas sp.Mutation(s): 0 
Gene Names: amnD
EC: 3.5.99.5
UniProt
Find proteins for Q9KWS2 (Pseudomonas sp)
Explore Q9KWS2 
Go to UniProtKB:  Q9KWS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KWS2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.871α = 90
b = 54.781β = 101.89
c = 134.594γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description