4ERA

Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Literature

Evidence for a Dual Role of an Active Site Histidine in alpha-Amino-beta-Carboxymuconate-epsilon-Semialdehyde Decarboxylase

Huo, L.Fielding, A.J.Chen, Y.Li, T.Iwaki, H.Hosler, J.P.Chen, L.Hasegawa, Y.Que, L.Liu, A.

(2012) Biochemistry 51: 5811-5821

  • DOI: https://doi.org/10.1021/bi300635b
  • Primary Citation of Related Structures:  
    4EPK, 4ERA, 4ERG, 4ERI

  • PubMed Abstract: 

    The previously reported crystal structures of α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD) show a five-coordinate Zn(II)(His)(3)(Asp)(OH(2)) active site. The water ligand is H-bonded to a conserved His228 residue adjacent to the metal center in ACMSD from Pseudomonas fluorescens (PfACMSD). Site-directed mutagenesis of His228 to tyrosine and glycine in this study results in a complete or significant loss of activity. Metal analysis shows that H228Y and H228G contain iron rather than zinc, indicating that this residue plays a role in the metal selectivity of the protein. As-isolated H228Y displays a blue color, which is not seen in wild-type ACMSD. Quinone staining and resonance Raman analyses indicate that the blue color originates from Fe(III)-tyrosinate ligand-to-metal charge transfer. Co(II)-substituted H228Y ACMSD is brown in color and exhibits an electron paramagnetic resonance spectrum showing a high-spin Co(II) center with a well-resolved (59)Co (I = 7/2) eight-line hyperfine splitting pattern. The X-ray crystal structures of as-isolated Fe-H228Y (2.8 Å) and Co-substituted (2.4 Å) and Zn-substituted H228Y (2.0 Å resolution) support the spectroscopic assignment of metal ligation of the Tyr228 residue. The crystal structure of Zn-H228G (2.6 Å) was also determined. These four structures show that the water ligand present in WT Zn-ACMSD is either missing (Fe-H228Y, Co-H228Y, and Zn-H228G) or disrupted (Zn-H228Y) in response to the His228 mutation. Together, these results highlight the importance of His228 for PfACMSD's metal specificity as well as maintaining a water molecule as a ligand of the metal center. His228 is thus proposed to play a role in activating the metal-bound water ligand for subsequent nucleophilic attack on the substrate.


  • Organizational Affiliation

    Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, P.O. Box 4098, Atlanta, GA 30303, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-amino-3-carboxymuconate 6-semialdehyde decarboxylase
A, B
334Pseudomonas fluorescensMutation(s): 1 
Gene Names: nbaD
UniProt
Find proteins for Q83V25 (Pseudomonas fluorescens)
Explore Q83V25 
Go to UniProtKB:  Q83V25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83V25
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.033α = 90
b = 90.033β = 90
c = 167.314γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description