1UHE

Crystal structure of aspartate decarboxylase, isoaspargine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase

Lee, B.I.Suh, S.W.

(2004) J.Mol.Biol. 340: 1-7

  • DOI: 10.1016/j.jmb.2004.04.049
  • Primary Citation of Related Structures:  
  • Also Cited By: 2C45

  • PubMed Abstract: 
  • l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4' ...

    l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A. We have determined the crystal structure of Helicobacter pylori ADC, a tetrameric enzyme, in two forms: the apo structure at 2.0 A resolution and the isoasparagine complex structure at 1.55 A resolution. All subunits of the tetramer are self-processed at the Gly24-Ser25 linkage, producing the smaller beta chain (residues 1-24) and the larger alpha chain (residues 25-117). Each subunit contains nine beta-strands and three alpha-helices; it is folded into the double-psi beta-barrel structure. In the apo structure, the new amino terminus of the alpha chain, Ser25, is converted into a pyruvoyl group. In the isoasparagine complex structure, the substrate analog is covalently attached to the pyruvoyl group. This structure represents the enzyme-substrate Schiff base intermediate that was proposed to form prior to the decarboxylation step in the catalytic cycle of ADC. Thus our study provides direct structural evidence for the reaction mechanism of ADC.


    Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase beta chain
B
24Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P56065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56065
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase alpha chain
A
97Helicobacter pylori (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P56065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56065
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NSN
Query on NSN

Download SDF File 
Download CCD File 
A
N~2~-(2-AMINO-1-METHYL-2-OXOETHYLIDENE)ASPARAGINATE
C7 H11 N3 O4
YZKQNDLOQTXCHV-BNTYAIEMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.206 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.826α = 90.00
b = 81.826β = 90.00
c = 93.777γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance