1W1Z

Structure of the plant like 5-Aminolaevulinic Acid Dehydratase from Chlorobium vibrioforme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.382 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution.

Coates, L.Beaven, G.Erskine, P.T.Beale, S.I.Avissar, Y.J.Gill, R.Mohammed, F.Wood, S.P.Shoolingin-Jordan, P.Cooper, J.B.

(2004) J. Mol. Biol. 342: 563-570

  • DOI: 10.1016/j.jmb.2004.07.007

  • PubMed Abstract: 
  • 5-Aminolaevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyses the dimerisation of 5-aminolaevulinic acid to form the pyrrole, porphobilinogen. ALAD from Chlorobium vibrioforme is shown to form a homo-o ...

    5-Aminolaevulinic acid dehydratase (ALAD), an early enzyme of the tetrapyrrole biosynthesis pathway, catalyses the dimerisation of 5-aminolaevulinic acid to form the pyrrole, porphobilinogen. ALAD from Chlorobium vibrioforme is shown to form a homo-octameric structure with 422 symmetry in which each subunit adopts a TIM-barrel fold with a 30 residue N-terminal arm extension. Pairs of monomers associate with their arms wrapped around each other. Four of these dimers interact principally via their arm regions to form octamers in which each active site is located on the surface. The active site contains two invariant lysine residues (200 and 253), one of which (Lys253) forms a Schiff base link with the bound substrate analogue, laevulinic acid. The carboxyl group of the laevulinic acid forms hydrogen bonds with the side-chains of Ser279 and Tyr318. The structure was examined to determine the location of the putative active-site magnesium ion, however, no evidence for the metal ion was found in the electron density map. This is in agreement with previous kinetic studies that have shown that magnesium stimulates but is not required for activity. A different site close to the active site flap, in which a putative magnesium ion is coordinated by a glutamate carboxyl and five solvent molecules may account for the stimulatory properties of magnesium ions on the enzyme.


    Organizational Affiliation

    School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. leighton@spymac.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DELTA-AMINOLEVULINIC ACID DEHYDRATASE
A, B
328Chlorobaculum parvum (strain NCIB 8327)Mutation(s): 0 
Gene Names: hemB
EC: 4.2.1.24
Find proteins for Q59334 (Chlorobaculum parvum (strain NCIB 8327))
Go to UniProtKB:  Q59334
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SHF
Query on SHF

Download SDF File 
Download CCD File 
A, B
LAEVULINIC ACID
LEVULINIC ACID
C5 H8 O3
JOOXCMJARBKPKM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.382 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 125.235α = 90.00
b = 125.235β = 90.00
c = 164.603γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SHELXrefinement
SCALEDdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-02
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-02-28
    Type: Database references, Source and taxonomy, Structure summary