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Literature summary extracted from

  • Roberts, A.; Gill, R.; Hussey, R.J.; Mikolajek, H.; Erskine, P.T.; Cooper, J.B.; Wood, S.P.; Chrystal, E.J.; Shoolingin-Jordan, P.M.
    Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme (2013), Acta Crystallogr. Sect. D, 69, 471-485.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.5.1.61 gene hemC, a single gene for PBGD in chromosome 5, recombinant expression of a codon-optimized PBGD gene in Escherichia coli Arabidopsis thaliana

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.5.1.61 purified recombinant enzyme with bound cofactor, crystallization in the dark due to light-sensitivity of the cofactor, hanging drop method, mixing of 5 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM DTT, with reservoir solution containing 25% w/v PEG 4000, 100 mM sodium citrate, pH 5.6, and 200 mM ammonium sulfate, X-ray diffraction structure determination and analysis at 1.45 A resolution, molecular modelling Arabidopsis thaliana

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.5.1.61 chloroplast in the chloroplast, the precursor is processed by the removal of an N-terminal transit peptide which is around 60 residues in length Arabidopsis thaliana 9507
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.5.1.61 4 porphobilinogen + H2O Arabidopsis thaliana
-
 hydroxymethylbilane + 4 NH3
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.5.1.61 Arabidopsis thaliana Q43316 gene hemC
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.5.1.61 recombinant enzyme from Escherichia coli by ion exchange chromatography and gel filtration Arabidopsis thaliana

Reaction

EC Number Reaction Comment Organism Reaction ID
2.5.1.61 4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3 four molecules of the pyrrole porphobilinogen are condensed to form the linear tetrapyrrole preuroporphyrinogen (hydroxymethylbilane). Hydrolysis of the linkage between the first substrate moiety and the cofactor releases the tetrapyrrole product preuroporphyrinogen Arabidopsis thaliana
a

Source Tissue

EC Number Source Tissue Comment Organism Textmining
2.5.1.61 leaf
-
 Arabidopsis thaliana
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.5.1.61 4 porphobilinogen + H2O
-
 Arabidopsis thaliana hydroxymethylbilane + 4 NH3
-
 ?

Subunits

EC Number Subunits Comment Organism
2.5.1.61 More three-dimensional structure analysis, molecular modelling, overview Arabidopsis thaliana

Synonyms

EC Number Synonyms Comment Organism
2.5.1.61 PBGD
-
 Arabidopsis thaliana
2.5.1.61 porphobilinogen deaminase
-
 Arabidopsis thaliana

Cofactor

EC Number Cofactor Comment Organism Structure
2.5.1.61 dipyrromethane the active site possesses the unusual dipyrromethane cofactor which is extended during the reaction by the sequential addition of the four substrate molecules. The cofactor is linked covalently to the enzyme through a thioether bridge to the invariant Cys254, binding structure, overview. Hydrolysis of the linkage between the first substrate moiety and the cofactor releases the tetrapyrrole product preuroporphyrinogen. The dipyrromethane cofactor of enzyme PBGD is light-sensitive Arabidopsis thaliana

General Information

EC Number General Information Comment Organism
2.5.1.61 metabolism the enzyme hydroxymethylbilane synthase catalyses a key early step of the heme and chlorophyll biosynthesis pathways in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole Arabidopsis thaliana