Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37.91 kDa 
• Atom Count: 3111 
• Modelled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 1

1YLV

SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID

• PDB DOI: 10.2210/pdb1YLV/pdb

• Classification: LYASE
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1999-02-22 Released: 2000-02-23 
• Deposition Author(s): Erskine, P.T., Newbold, R., Roper, J., Coker, A., Warren, M.J., Shoolingin-Jordan, P.M., Wood, S.P., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.265 
• R-Value Work: 0.207 

Literature

The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid.

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

(1999) Protein Sci 8: 1250-1256

• PubMed: 10386874 
• DOI: 10.1110/ps.8.6.1250
• Primary Citation of Related Structures:  
  1YLV


• PubMed Abstract: 
  

The X-ray structure of the complex formed between yeast 5-aminolaevulinic acid dehydratase (ALAD) and the inhibitor laevulinic acid has been determined at 2.15 A resolution. The inhibitor binds by forming a Schiff base link with one of the two invariant lysines at the catalytic center: Lys263. It is known that this lysine forms a Schiff base link with substrate bound at the enzyme's so-called P-site. The carboxyl group of laevulinic acid makes hydrogen bonds with the side-chain-OH groups of Tyr329 and Ser290, as well as with the main-chain >NH group of Ser290. The aliphatic moiety of the inhibitor makes hydrophobic interactions with surrounding aromatic residues in the protein including Phe219, which resides in the flap covering the active site. Our analysis strongly suggests that the same interactions will be made by P-side substrate and also indicates that the substrate that binds at the enzyme's A-site will interact with the enzyme's zinc ion bound by three cysteines (133, 135, and 143). Inhibitor binding caused a substantial ordering of the active site flap (residues 217-235), which was largely invisible in the native electron density map and indicates that this highly conserved yet flexible region has a specific role in substrate binding during catalysis.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (5-AMINOLAEVULINIC 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
SHF	C [auth A]	LAEVULINIC ACID C5 H8 O3 JOOXCMJARBKPKM-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SHF	PDBBind:  1YLV	Ki: 2.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.265 
• R-Value Work: 0.207 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 103.4	β = 90
c = 168	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
CCP4	refinement
XDS	data reduction
CCP4	data scaling
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-22 
• Released Date: 2000-02-23 
Deposition Author(s): Erskine, P.T., Newbold, R., Roper, J., Coker, A., Warren, M.J., Shoolingin-Jordan, P.M., Wood, S.P., Cooper, J.B.

Revision History  

• Version 1.0: 2000-02-23
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2018-04-11
  Changes: Data collection