PDBsum entry 1w31

Go to PDB code: 
protein ligands metals links
Lyase PDB id
Protein chain
340 a.a. *
Waters ×269
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Yeast 5-aminolaevulinic acid dehydratase 5-hydroxylaevulinic acid complex
Structure: Delta-aminolevulinic acid dehydratase. Chain: a. Synonym: 5-aminolaevulinic acid dehydratase, aladh. Engineered: yes. Other_details: complex with 5-hydroxylaevulinic acid
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: ns1(jm109/pns1). Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Octamer (from PDB file)
1.90Å     R-factor:   0.189     R-free:   0.249
Authors: P.T.Erskine,L.Coates,R.Newbold,A.A.Brindley,F.Stauffer, G.D.E.Beaven,R.Gill,S.P.Wood,M.J.Warren,J.B.Cooper, P.M.Shoolingin-Jordan,R.Neier
Key ref:
P.T.Erskine et al. (2005). Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid. Acta Crystallogr D Biol Crystallogr, 61, 1222-1226. PubMed id: 16131755 DOI: 10.1107/S0907444905018834
11-Jul-04     Release date:   23-Aug-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05373  (HEM2_YEAST) -  Delta-aminolevulinic acid dehydratase
342 a.a.
340 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Porphobilinogen synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Porphyrin Biosynthesis (early stages)
      Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O
2 × 5-aminolevulinate
Bound ligand (Het Group name = SHO)
matches with 70.00% similarity
= porphobilinogen
+ 2 × H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     tetrapyrrole biosynthetic process   4 terms 
  Biochemical function     catalytic activity     6 terms  


    Added reference    
DOI no: 10.1107/S0907444905018834 Acta Crystallogr D Biol Crystallogr 61:1222-1226 (2005)
PubMed id: 16131755  
Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid.
P.T.Erskine, L.Coates, R.Newbold, A.A.Brindley, F.Stauffer, G.D.Beaven, R.Gill, A.Coker, S.P.Wood, M.J.Warren, P.M.Shoolingin-Jordan, R.Neier, J.B.Cooper.
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).
  Selected figure(s)  
Figure 1.
Figure 1 The reaction catalysed by 5-aminolaevulinic acid dehydratase (ALAD). Two molecules of 5-aminolaevulinic acid (ALA) are condensed to form the pyrrole porphobilinogen (PBG).
Figure 2.
Figure 2 (a) A ribbon diagram of the TIM-barrel fold of the ALAD monomer with its pronounced N-terminal arm and two active-site lysines shown in ball-and-stick representation. (b) The assembly of ALAD monomers (coloured differently) to form dimers and (c) the organization of the functional ALAD octamer. This figure and others similar were prepared using the programs MOLSCRIPT (Kraulis, 1991 [Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]-[bluearr.gif] ) and BOBSCRIPT (Esnouf, 1997 [Esnouf, R. (1997). J. Mol. Graph. Model. 15, 132.]-[bluearr.gif] ).
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1222-1226) copyright 2005.  
  Figures were selected by an automated process.