4IFK

Arginines 51 and 239* from a Neighboring Subunit are Essential for Catalysis in a Zinc-dependent Decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.012 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


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Literature

The power of two: arginine 51 and arginine 239* from a neighboring subunit are essential for catalysis in alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase.

Huo, L.Davis, I.Chen, L.Liu, A.

(2013) J.Biol.Chem. 288: 30862-30871

  • DOI: 10.1074/jbc.M113.496869
  • Primary Citation of Related Structures:  4IFO, 4IFR, 4IG2

  • PubMed Abstract: 
  • Although the crystal structure of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase from Pseudomonas fluorescens was solved as a dimer, this enzyme is a mixture of monomer, dimer, and higher order structures in solution. In this work, we found t ...

    Although the crystal structure of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase from Pseudomonas fluorescens was solved as a dimer, this enzyme is a mixture of monomer, dimer, and higher order structures in solution. In this work, we found that the dimeric state, not the monomeric state, is the functionally active form. Two conserved arginine residues are present in the active site: Arg-51 and an intruding Arg-239* from the neighboring subunit. In this study, they were each mutated to alanine and lysine, and all four mutants were catalytically inactive. The mutants were also incapable of accommodating pyridine-2,6-dicarboxylic acid, a competitive inhibitor of the native enzyme, suggesting that the two Arg residues are involved in substrate binding. It was also observed that the decarboxylase activity was partially recovered in a heterodimer hybridization experiment when inactive R51(A/K) and R239(A/K) mutants were mixed together. Of the 20 crystal structures obtained from mixing inactive R51A and R239A homodimers that diffracted to a resolution lower than 3.00 Å, two structures are clearly R51A/R239A heterodimers and belong to the C2 space group. They were refined to 1.80 and 2.00 Å resolutions, respectively. Four of the remaining crystals are apparently single mutants and belong to the P42212 space group. In the heterodimer structures, one active site is shown to contain dual mutation of Ala-51 and Ala-239*, whereas the other contains the native Arg-51 and Arg-239* residues, identical to the wild-type structure. Thus, these observations provide the foundation for a molecular mechanism by which the oligomerization state of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase could regulate the enzyme activity.


    Organizational Affiliation

    From the Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
A
331Pseudomonas fluorescensGene Names: nbaD
Find proteins for Q83V25 (Pseudomonas fluorescens)
Go to UniProtKB:  Q83V25
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
B
331Pseudomonas fluorescensGene Names: nbaD
Find proteins for Q83V25 (Pseudomonas fluorescens)
Go to UniProtKB:  Q83V25
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.012 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.848α = 90.00
b = 49.062β = 127.10
c = 110.545γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing
MAR345dtbdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Database references