1EB3

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7-DIOXOSEBACIC ACID COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.308 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Two Diacid Inhibitors

Erskine, P.T.Coates, L.Newbold, R.Brindley, A.A.Stauffer, F.Wood, S.P.Warren, M.J.Cooper, J.B.Shoolingin-Jordan, P.M.Neier, R.

(2001) FEBS Lett. 503: 196

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of 5-aminolaevulinic acid dehydratase complexed with two irreversible inhibitors (4-oxosebacic acid and 4,7-dioxosebacic acid) have been solved at high resolution. Both inhibitors bind by forming a Schiff base link with Lys 263 at the ...

    The structures of 5-aminolaevulinic acid dehydratase complexed with two irreversible inhibitors (4-oxosebacic acid and 4,7-dioxosebacic acid) have been solved at high resolution. Both inhibitors bind by forming a Schiff base link with Lys 263 at the active site. Previous inhibitor binding studies have defined the interactions made by only one of the two substrate moieties (P-side substrate) which bind to the enzyme during catalysis. The structures reported here provide an improved definition of the interactions made by both of the substrate molecules (A- and P-side substrates). The most intriguing result is the novel finding that 4,7-dioxosebacic acid forms a second Schiff base with the enzyme involving Lys 210. It has been known for many years that P-side substrate forms a Schiff base (with Lys 263) but until now there has been no evidence that binding of A-side substrate involves formation of a Schiff base with the enzyme. A catalytic mechanism involving substrate linked to the enzyme through Schiff bases at both the A- and P-sites is proposed.


    Organizational Affiliation

    Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-AMINOLAEVULINIC ACID DEHYDRATASE
A
340Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HEM2
EC: 4.2.1.24
Find proteins for P05373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05373
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DSB
Query on DSB

Download SDF File 
Download CCD File 
A
4,7-DIOXOSEBACIC ACID
C10 H14 O6
DUAWJQCMZICMIK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.308 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 104.300α = 90.00
b = 104.300β = 90.00
c = 167.200γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
MOSFLMdata reduction
SHELXL-97refinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance