PDBsum entry 1ohl

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Lyase PDB id
Protein chain
340 a.a. *
Waters ×342
* Residue conservation analysis
PDB id:
Name: Lyase
Title: Yeast 5-aminolaevulinic acid dehydratase putative cyclic reaction intermediate complex
Structure: Delta-aminolevulinic acid dehydratase. Chain: a. Synonym: aladh, porphobilinogen synthase. Engineered: yes. Other_details: co-crystallisation with substrate aminolaevulinic 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)
1.6Å     R-factor:   0.188     R-free:   0.241
Authors: P.T.Erskine,L.Coates,D.Butler,J.H.Youell,A.A.Brindley, S.P.Wood,M.J.Warren,P.M.Shoolingin-Jordan,J.B.Cooper
Key ref: P.T.Erskine et al. (2003). X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase. Biochem J, 373, 733-738. PubMed id: 12777167 DOI: 10.1042/BJ20030513
27-May-03     Release date:   02-Jun-03    
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 = PBG)
corresponds exactly
+ 2 × H(2)O
      Cofactor: Zinc
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: 10.1042/BJ20030513 Biochem J 373:733-738 (2003)
PubMed id: 12777167  
X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.
P.T.Erskine, L.Coates, D.Butler, J.H.Youell, A.A.Brindley, S.P.Wood, M.J.Warren, P.M.Shoolingin-Jordan, J.B.Cooper.
The X-ray structure of yeast 5-aminolaevulinic acid dehydratase, in which the catalytic site of the enzyme is complexed with a putative cyclic intermediate composed of both substrate moieties, has been solved at 0.16 nm (1.6 A) resolution. The cyclic intermediate is bound covalently to Lys(263) with the amino group of the aminomethyl side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The cyclic intermediate is catalytically competent, as shown by its turnover in the presence of added substrate to form porphobilinogen. The findings, combined with those of previous studies, are consistent with a catalytic mechanism in which the C-C bond linking both substrates in the intermediate is formed before the C-N bond.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20506125 G.Layer, J.Reichelt, D.Jahn, and D.W.Heinz (2010).
Structure and function of enzymes in heme biosynthesis.
  Protein Sci, 19, 1137-1161.  
17893767 A.Gumm, A.Hammershøi, M.Kofod-Hansen, O.Mønsted, and H.Osholm Sørensen (2007).
First aminoacetone chelate: [Co(tren){NH2CH2C(O)CH3}]3+-a substrate binding and activation model for zinc(II)-dependent 5-aminolaevulinic acid dehydratase.
  Dalton Trans, (), 3227-3231.  
16304458 L.Coates, G.Beaven, P.T.Erskine, S.I.Beale, S.P.Wood, P.M.Shoolingin-Jordan, and J.B.Cooper (2005).
Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor.
  Acta Crystallogr D Biol Crystallogr, 61, 1594-1598.
PDB code: 2c1h
15710608 L.Tang, L.Stith, and E.K.Jaffe (2005).
Substrate-induced interconversion of protein quaternary structure isoforms.
  J Biol Chem, 280, 15786-15793.  
16131755 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, and J.B.Cooper (2005).
Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid.
  Acta Crystallogr D Biol Crystallogr, 61, 1222-1226.
PDB code: 1w31
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