1AW5

5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.

Erskine, P.T.Senior, N.Awan, S.Lambert, R.Lewis, G.Tickle, I.J.Sarwar, M.Spencer, P.Thomas, P.Warren, M.J.Shoolingin-Jordan, P.M.Wood, S.P.Cooper, J.B.

(1997) Nat Struct Biol 4: 1025-1031

  • DOI: 10.1038/nsb1297-1025
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 5-Aminolaevulinate dehydratase (ALAD) is a homo-octameric metallo-enzyme that catalyses the formation of porphobilinogen from 5-aminolaevulinic acid. The structure of the yeast enzyme has been solved to 2.3 A resolution, revealing that each subunit a ...

    5-Aminolaevulinate dehydratase (ALAD) is a homo-octameric metallo-enzyme that catalyses the formation of porphobilinogen from 5-aminolaevulinic acid. The structure of the yeast enzyme has been solved to 2.3 A resolution, revealing that each subunit adopts a TIM barrel fold with a 39 residue N-terminal arm. Pairs of monomers wrap their arms around each other to form compact dimers and these associate to form a 422 symmetric octamer. All eight active sites are on the surface of the octamer and possess two lysine residues (210 and 263), one of which, Lys 263, forms a Schiff base link to the substrate. The two lysine side chains are close to two zinc binding sites one of which is formed by three cysteine residues (133, 135 and 143) while the other involves Cys 234 and His 142. ALAD has features at its active site that are common to both metallo- and Schiff base-aldolases and therefore represents an intriguing combination of both classes of enzyme. Lead ions, which inhibit ALAD potently, replace the zinc bound to the enzyme's unique triple-cysteine site.


    Organizational Affiliation

    School of Biological Sciences, University of Southampton, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-AMINOLEVULINATE DEHYDRATASEA340Saccharomyces cerevisiaeMutation(s): 5 
Gene Names: HEM2
EC: 4.2.1.24
Find proteins for P05373 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05373 
Go to UniProtKB:  P05373
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Observed: 0.198 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.5α = 90
b = 102.5β = 90
c = 168.3γ = 90
Software Package:
Software NamePurpose
DMmodel building
MLPHAREphasing
VECSUMmodel building
RESTRAINrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
DMphasing
VECSUMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-09-13
    Changes: Refinement description