1W31

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1W31/pdb

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


• Deposited: 2004-07-11 Released: 2005-08-23 
• Deposition Author(s): Erskine, P.T., Coates, L., Newbold, R., Brindley, A.A., Stauffer, F., Beaven, G.D.E., Gill, R., Wood, S.P., Warren, M.J., Cooper, J.B., Shoolingin-Jordan, P.M., Neier, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.190 

Literature

Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with the Inhibitor 5-Hydroxylaevulinic Acid

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

(2005) Acta Crystallogr D Biol Crystallogr 61: 1222

• PubMed: 16131755 
• DOI: https://doi.org/10.1107/S0907444905018834
• Primary Citation of Related Structures:  
  1W31


• PubMed Abstract: 
  

  The X-ray structure of the enzyme 5-aminolaevulinic acid dehydratase (ALAD) from yeast complexed with the competitive inhibitor 5-hydroxylaevulinic acid has been determined at a resolution of 1.9 A. The structure shows that the inhibitor is bound by a Schiff-base link to one of the invariant active-site lysine residues (Lys263). The inhibitor appears to bind in two well defined conformations and the interactions made by it suggest that it is a very close analogue of the substrate 5-aminolaevulinic acid (ALA).

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Organizational Affiliation: 

School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, England.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
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: 2,960 
• Modelled Residue Count: 340 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA-AMINOLEVULINIC ACID DEHYDRATASE	A	342	Saccharomyces cerevisiae	Mutation(s): 0  EC: 4.2.1.24
UniProt
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
SHO	B [auth A]	5-HYDROXYLAEVULINIC ACID C5 H10 O3 PHOJOSOUIAQEDH-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SHO	Binding MOAD:  1W31	Ki: 2.50e+5 (nM) from 1 assay(s)
	PDBBind:  1W31	Ki: 2.50e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.249 
• R-Value Work: 0.190 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.57	α = 90
b = 102.57	β = 90
c = 168.38	γ = 90

Software Package:

Software Name	Purpose
RESTRAIN	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-23 
Deposition Author(s): Erskine, P.T., Coates, L., Newbold, R., Brindley, A.A., Stauffer, F., Beaven, G.D.E., Gill, R., Wood, S.P., Warren, M.J., Cooper, J.B., Shoolingin-Jordan, P.M., Neier, R.

Revision History  

• Version 1.0: 2005-08-23
  Type: Initial release
  
• Version 1.1: 2014-08-13
  Changes: Derived calculations, Other, Refinement description, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.3: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description