HemB (PA5243) is the porphobilinogen synthase (5-aminolevulinate dehydratase, EC 4.2.1.24) of Pseudomonas aeruginosa. It condenses two molecules of 5-aminolevulinate in an aldol-like reaction to form porphobilinogen, the first pyrrole and the first committed step of tetrapyrrole biosynthesis, which in this organism supplies heme and the other tetrapyrrole cofactors. The enzyme is a cytoplasmic Mg2+-dependent homooctamer formed from dimers; many crystal structures with substrate analogues and inhibitors, including one showing Mg2+ in the active site, support a mechanism that begins with C-C bond formation between the two substrate molecules. The gene was cloned by complementation of an E. coli hemB mutant and is not obviously regulated by oxygen, nitrate, heme or iron.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004655 porphobilinogen synthase activity | EXP PMID:16819823 Probing the active site of Pseudomonas aeruginosa porphobili... | ACCEPT | Summary: UniProt EXP: kinetic and structural study of the purified P. aeruginosa enzyme with reaction-intermediate analogues. Reason: Direct biochemical evidence for the core activity. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway file:PSEAE/hemB/hemB-uniprot.txt Reaction=2 5-aminolevulinate = porphobilinogen + 2 H2O + H(+) |
| GO:0004655 porphobilinogen synthase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000156046 (ALAD family, nine seeds: E. coli HemB, human ALAD P13716, bovine, mouse, rat, yeast HEM2, fly, Plasmodium and HemB itself). The self-seed reflects the gene's own experimental rows. Reason: Ancient, uniformly conserved activity; the IBD is well seeded. Supporting Evidence: PMID:9529530 P. aeruginosa hemB was overexpressed in an E. coli hemB mutant using the phage T7 RNA polymerase system and its Mg(2+)-dependent activity was directly demonstrated file:PSEAE/hemB/hemB-uniprot.txt Reaction=2 5-aminolevulinate = porphobilinogen + 2 H2O + H(+) |
| GO:0004655 porphobilinogen synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro/EC/RHEA mapping; same claim as the experimental rows. Reason: Consistent with direct biochemical evidence. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway |
| GO:0004655 porphobilinogen synthase activity | IMP PMID:9529530 Cloning, mapping and functional characterization of the hemB... | ACCEPT | Summary: PseudoCAP IMP and one of nine seeds of the PTN000156046 IBD. The gene was cloned by complementation of an E. coli hemB mutant and Mg2+-dependent ALAD activity was measured directly after overexpression. Reason: Seed is SOUND. The activity was demonstrated directly (IDA would fit as well as IMP), and the complementation agrees. Supporting Evidence: PMID:9529530 P. aeruginosa hemB was overexpressed in an E. coli hemB mutant using the phage T7 RNA polymerase system and its Mg(2+)-dependent activity was directly demonstrated PMID:9529530 The hemB gene was cloned from Pseudomonas aeruginosa by functional complementation of an E. coli hemB mutant |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA cytosol from PTN000156046, seeded by E. coli HemB and mouse Alad. Reason: Soluble octameric enzyme with no signal peptide; cytosolic location is expected. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway |
| GO:0006779 porphyrin-containing compound biosynthetic process | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA-based IEA porphyrin-containing compound biosynthetic process. Reason: Porphobilinogen is the precursor of all porphyrins (heme) as well as of other tetrapyrroles, so this broader process term is as precise as the branch-point position of the enzyme warrants. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway PMID:9529530 The hemB gene was cloned from Pseudomonas aeruginosa by functional complementation of an E. coli hemB mutant |
| GO:0006779 porphyrin-containing compound biosynthetic process | IMP PMID:9529530 Cloning, mapping and functional characterization of the hemB... | ACCEPT | Summary: PseudoCAP IMP from complementation of the E. coli hemB mutant. Reason: True and appropriately broad for the enzyme that makes the first pyrrole. Supporting Evidence: PMID:9529530 The hemB gene was cloned from Pseudomonas aeruginosa by functional complementation of an E. coli hemB mutant PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway |
| GO:0006783 heme biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA heme biosynthetic process from PTN000156046, seeded by mammalian, yeast, Plasmodium and E. coli enzymes. Reason: Heme is the main end product of the pathway that porphobilinogen enters. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway file:PSEAE/hemB/hemB-uniprot.txt Reaction=2 5-aminolevulinate = porphobilinogen + 2 H2O + H(+) |
| GO:0033014 tetrapyrrole biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping (IPR001731 ALAD) to tetrapyrrole biosynthetic process. Reason: Exactly the scope of the enzyme, which catalyses the first committed step of tetrapyrrole synthesis. Supporting Evidence: PMID:16819823 Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO metal ion binding. Reason: True but general. The P. aeruginosa enzyme is Mg2+-dependent and Mg2+ is seen in the active site, so the specific term is magnesium ion binding. Proposed replacements: magnesium ion binding Supporting Evidence: PMID:16819823 one of the determined protein structures provides for the first time structural evidence of a magnesium ion in the active site file:PSEAE/hemB/hemB-uniprot.txt Name=Mg(2+); Xref=ChEBI:CHEBI:18420; PMID:9529530 P. aeruginosa hemB was overexpressed in an E. coli hemB mutant using the phage T7 RNA polymerase system and its Mg(2+)-dependent activity was directly demonstrated |
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