Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 37.97 kDa 
• Atom Count: 3047 
• Modelled Residue Count: 340 
• Deposited Residue Count: 342 
• Unique protein chains: 1

1H7N

SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID AT 1.6 A RESOLUTION

• DOI: 10.2210/pdb1H7N/pdb

• Classification: DEHYDRATASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-07-09 Released: 2001-07-10 
• Deposition Author(s): Erskine, P.T., Newbold, R., Brindley, A.A., Wood, S.P., Shoolingin-Jordan, P.M., Warren, M.J., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.265 
• R-Value Observed: 0.217 

Literature

The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Substrate and Three Inhibitors

Erskine, P.T., Newbold, R., Brindley, A.A., Wood, S.P., Shoolingin-Jordan, P.M., Warren, M.J., Cooper, J.B.

(2001) J Mol Biol 312: 133

• PubMed: 11545591 
• DOI: 10.1006/jmbi.2001.4947
• Primary Citation of Related Structures:  
  1H7R, 1H7P, 1H7O, 1H7N


• PubMed Abstract: 
  

The structures of 5-aminolaevulinic acid dehydratase (ALAD) complexed with substrate (5-aminolaevulinic acid) and three inhibitors: laevulinic acid, succinylacetone and 4-keto-5-aminolaevulinic acid, have been solved at high resolution. The ligands all bind by forming a covalent link with Lys263 at the active site. The structures define the interactions made by one of the two substrate moieties that bind to the enzyme during catalysis. All of the inhibitors induce a significant ordering of the flap covering the active site. Succinylacetone appears to be unique by inducing a number of conformational changes in loops covering the active site, which may be important for understanding the co-operative properties of ALAD enzymes. Succinylacetone is produced in large amounts by patients suffering from the hereditary disease type I tyrosinaemia and its potent inhibition of ALAD also has implications for the pathology of this disease. The most intriguing result is that obtained with 4-keto-5-amino-hexanoic acid, which seems to form a stable carbinolamine intermediate with Lys263. It appears that we have defined the structure of an intermediate of Schiff base formation that the substrate forms upon binding to the P-site of the enzyme.

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Organizational Affiliation: 

Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-AMINOLAEVULINIC ACID DEHYDRATASE	A	342	Saccharomyces cerevisiae	Mutation(s): 0  EC: 4.2.1.24
Find proteins for P05373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05373  Go to UniProtKB:  P05373

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SHF	B [auth A]	LAEVULINIC ACID C5 H8 O3 JOOXCMJARBKPKM-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.265 
• R-Value Observed: 0.217 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.2	α = 90
b = 103.2	β = 90
c = 167.7	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
MOSFLM	data reduction
Agrovata	data scaling
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-07-09 
• Released Date: 2001-07-10 
Deposition Author(s): Erskine, P.T., Newbold, R., Brindley, A.A., Wood, S.P., Shoolingin-Jordan, P.M., Warren, M.J., Cooper, J.B.

Revision History  

• Version 1.0: 2001-07-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-22
  Changes: Data collection, Derived calculations, Other, Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection