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 
  • R-Value Observed: 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:  
    1UHE, 1UHD

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate 1-decarboxylase beta chainB24Helicobacter pyloriMutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P56065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56065 
Go to UniProtKB:  P56065
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate 1-decarboxylase alpha chainA97Helicobacter pyloriMutation(s): 0 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P56065 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56065 
Go to UniProtKB:  P56065
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NSN
Query on NSN

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 
  • R-Value Observed: 0.206 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.826α = 90
b = 81.826β = 90
c = 93.777γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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