7BZV

Crystal structure of 2-aminomuconic 6-semialdehyde dehydrogenase from Pseudomonas species AP-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

The tetrameric assembly of 2-aminomuconic 6-semialdehyde dehydrogenase is a functional requirement of cofactor NAD + binding.

Shi, Q.Chen, Y.Li, X.Dong, H.Chen, C.Zhong, Z.Yang, C.Liu, G.Su, D.

(2021) Environ Microbiol 

  • DOI: https://doi.org/10.1111/1462-2920.15840
  • Primary Citation of Related Structures:  
    7BZV

  • PubMed Abstract: 

    The bacterium Pseudomonas sp. AP-3 is able to use the environmental pollutant 2-aminophenol as its sole source of carbon, nitrogen, and energy. Eight genes (amnA, B, C, D, E, F, G, and H) encoding 2-aminophenol metabolizing enzymes are clustered into a single operon. 2-Aminomuconic 6-semialdehyde dehydrogenase (AmnC), a member of the aldehyde dehydrogenase (ALDH) superfamily, is responsible for oxidizing 2-aminomuconic 6-semialdehyde to 2-aminomuconate. In contrast to many other members of the ALDH superfamily, the structural basis of the catalytic activity of AmnC remains elusive. Here, we present the crystal structure of AmnC, which displays a homotetrameric quaternary assembly that is directly involved in its enzymatic activity. The tetrameric state of AmnC in solution was also presented using small-angle X-ray scattering. The tetramerization of AmnC is mediated by the assembly of a protruding hydrophobic beta-strand motif and residues V121 and S123 located in the NAD + -binding domain of each subunit. Dimeric mutants of AmnC dramatically lose NAD + binding affinity and failed to oxidize the substrate analogue 2-hydroxymuconate-6-semialdehyde to α-hydroxymuconic acid, indicating that tetrameric assembly of AmnC is functional requirement.


  • Organizational Affiliation

    State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-aminomuconic 6-semialdehyde dehydrogenase
A, B
492Pseudomonas sp.Mutation(s): 0 
Gene Names: amnC
EC: 1.2.1.32
UniProt
Find proteins for Q9KWS5 (Pseudomonas sp)
Explore Q9KWS5 
Go to UniProtKB:  Q9KWS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KWS5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG (Subject of Investigation/LOI)
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth B],
K [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
H [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.526α = 90
b = 181.526β = 90
c = 181.157γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0505903

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 2.0: 2024-06-19
    Changes: Advisory, Data collection, Database references, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary