3N2O

X-ray crystal structure of arginine decarboxylase complexed with Arginine from Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

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This is version 1.2 of the entry. See complete history


Literature

Evolution of substrate specificity within a diverse family of beta/alpha-barrel-fold basic amino acid decarboxylases: X-ray structure determination of enzymes with specificity for L-arginine and carboxynorspermidine.

Deng, X.Lee, J.Michael, A.J.Tomchick, D.R.Goldsmith, E.J.Phillips, M.A.

(2010) J Biol Chem 285: 25708-25719

  • DOI: 10.1074/jbc.M110.121137
  • Primary Citation of Related Structures:  
    3N29, 3N2O

  • PubMed Abstract: 
  • Pyridoxal 5'-phosphate (PLP)-dependent basic amino acid decarboxylases from the beta/alpha-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2 ...

    Pyridoxal 5'-phosphate (PLP)-dependent basic amino acid decarboxylases from the beta/alpha-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2.3- and 2.0-A resolution, solved as product complexes with agmatine and norspermidine. Despite low overall sequence identity, the monomeric and dimeric structures are similar to other enzymes in the family, with the active sites formed between the beta/alpha-barrel domain of one subunit and the beta-barrel of the other. ADC contains both a unique interdomain insertion (4-helical bundle) and a C-terminal extension (3-helical bundle) and it packs as a tetramer in the asymmetric unit with the insertions forming part of the dimer and tetramer interfaces. Analytical ultracentrifugation studies confirmed that the ADC solution structure is a tetramer. Specificity for different basic amino acids appears to arise primarily from changes in the position of, and amino acid replacements in, a helix in the beta-barrel domain we refer to as the "specificity helix." Additionally, in CANSDC a key acidic residue that interacts with the distal amino group of other substrates is replaced by Leu(314), which interacts with the aliphatic portion of norspermidine. Neither product, agmatine in ADC nor norspermidine in CANSDC, form a Schiff base to pyridoxal 5'-phosphate, suggesting that the product complexes may promote product release by slowing the back reaction. These studies provide insight into the structural basis for the evolution of novel function within a common structural-fold.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Biosynthetic arginine decarboxylaseA, B, C, D648Vibrio vulnificus YJ016Mutation(s): 0 
Gene Names: ADCspeAVV1986
EC: 4.1.1.19
UniProt
Find proteins for Q7MK24 (Vibrio vulnificus (strain YJ016))
Explore Q7MK24 
Go to UniProtKB:  Q7MK24
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.648α = 90
b = 119.365β = 96.3
c = 121.84γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
SHELXDphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-02-22
    Changes: Database references