HemB is one of two KT2440 delta-aminolevulinate dehydratase paralogs. It is an ALAD-family enzyme predicted to condense two 5-aminolevulinate molecules into porphobilinogen. Sequence-based site annotation identifies catalytic zinc ligands, a magnesium-binding site, and the conserved lysines that form Schiff-base intermediates, supporting a metal-dependent porphobilinogen synthase role in heme-b precursor synthesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004655 porphobilinogen synthase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the specific predicted catalytic function of HemB. Reason: UniProt assigns EC 4.2.1.24, the ALAD family, conserved catalytic Schiff-base sites, and metal-binding residues consistent with porphobilinogen synthase activity. Support is family/domain membership (Pfam ALAD, PIRSF porphobilinogen synthase, PROSITE ALAD active-site signature) plus PIRSR-predicted Schiff-base lysines; the protein has not been assayed. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt DR PIRSF; PIRSF001415; Porphbilin_synth; 1. file:PSEPK/hemB/hemB-uniprot.txt DR PROSITE; PS00169; D_ALA_DEHYDRATASE; 1. file:PSEPK/hemB/hemB-uniprot.txt /note="Schiff-base intermediate with substrate" |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: A soluble cytosolic location is consistent with the ALAD-family architecture. Reason: The UniProt record has no SIGNAL, TRANSMEM or Phobius/SignalP (SAM) features and no CC SUBCELLULAR LOCATION comment; ALAD-family porphobilinogen synthases are soluble homo-oligomeric enzymes. The cytosol call therefore rests on the absence of export/membrane signals plus family membership, not on a localization assay. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt DR Pfam; PF00490; ALAD; 1. |
| GO:0006779 porphyrin-containing compound biosynthetic process | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: This is a correct broad pathway assignment for an early shared tetrapyrrole step. Reason: Porphobilinogen formation supplies the common tetrapyrrole trunk. The annotation is biologically correct, but the catalytic activity and direct tetrapyrrole-biosynthesis role are more informative core claims. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt PATHWAY: Porphyrin-containing compound metabolism; protoporphyrin-IX |
| GO:0006783 heme biosynthetic process | IEA GO_REF:0000118 | ACCEPT | Summary: ALAD activity supplies porphobilinogen to the shared heme-b pathway. Reason: The reaction is required upstream of hydroxymethylbilane, uroporphyrinogen III, and all subsequent heme-b intermediates. The process call is inferred from family membership (porphobilinogen synthase family, CDD ALAD_PBGS), not from a KT2440 mutant. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt DR CDD; cd00384; ALAD_PBGS; 1. file:PSEPK/hemB/hemB-uniprot.txt DR PIRSF; PIRSF001415; Porphbilin_synth; 1. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000118 | ACCEPT | Summary: HemB contains a predicted catalytic zinc site characteristic of one ALAD lineage. Reason: Three residues are annotated as catalytic Zn2+ ligands, and the sequence contains the corresponding cysteine-rich region. This architecture is absent from the KT2440 HemBB paralog. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt ligand_note="catalytic" |
| GO:0033014 tetrapyrrole biosynthetic process | IEA GO_REF:0000002 | ACCEPT | Summary: HemB directly participates in tetrapyrrole biosynthesis. Reason: ALAD produces porphobilinogen for the shared tetrapyrrole trunk, so the broad process term is accurate and does not force a single downstream tetrapyrrole endpoint. Support is membership in the porphobilinogen synthase (ALAD) family, whose product is the tetrapyrrole precursor. Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt DR PIRSF; PIRSF001415; Porphbilin_synth; 1. file:PSEPK/hemB/hemB-uniprot.txt DR InterPro; IPR001731; ALAD. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: The broad metal call can be replaced by the additional predicted magnesium site. Reason: Zinc binding is already represented by GO:0008270, while UniProt also identifies a distinct Mg2+-binding residue. GO:0000287 records that second metal requirement without retaining a generic parent term. Proposed replacements: magnesium ion binding Supporting Evidence: file:PSEPK/hemB/hemB-uniprot.txt ligand="Mg(2+)" |
Loading supporting content…
Download this section (compressed HTML)Q: Is HemB the principal aerobic ALAD isozyme, and how does its zinc site affect activity relative to HemBB?
Experiment: Purify both proteins and compare kinetics, oligomerization, and metal dependence, then phenotype single and double mutants with ALA rescue.
Hypothesis: HemB and HemBB are active ALAD paralogs with different metal dependence.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)