hemD

UniProt ID: Q88RE4
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: COMPLETE
Aliases:
PP_0187
📝 Provide Detailed Feedback

Gene Description

HemD is uroporphyrinogen-III synthase. It cyclizes the linear HemC product hydroxymethylbilane with inversion of the terminal pyrrole ring to generate uroporphyrinogen III, the common branch-point tetrapyrrole used for heme and other modified tetrapyrroles.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004852 uroporphyrinogen-III synthase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: This is the specific catalytic function predicted for HemD.
Reason: UniProt assigns EC 4.2.1.75 and describes cyclization and terminal-ring inversion of hydroxymethylbilane to uroporphyrinogen III.
Supporting Evidence:
file:PSEPK/hemD/hemD-uniprot.txt
Catalyzes cyclization of the linear tetrapyrrole,
GO:0006780 uroporphyrinogen III biosynthetic process
IEA
GO_REF:0000120 		ACCEPT
Summary: HemD directly produces uroporphyrinogen III.
Reason: This process term exactly matches the product-forming role of HemD and is preferable to broader tetrapyrrole-process terms.
Supporting Evidence:
file:PSEPK/hemD/hemD-uniprot.txt
Reaction=hydroxymethylbilane = uroporphyrinogen III + H2O;
GO:0033014 tetrapyrrole biosynthetic process
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: This broad process parent is correct but less informative than the product-specific term.
Reason: HemD directly participates in tetrapyrrole synthesis, while GO:0006780 more precisely captures formation of its uroporphyrinogen III product.
Supporting Evidence:
file:PSEPK/hemD/hemD-uniprot.txt
Reaction=hydroxymethylbilane = uroporphyrinogen III + H2O;

Core Functions

Cyclizes hydroxymethylbilane with ring inversion to form uroporphyrinogen III, the shared tetrapyrrole precursor for heme b.

Molecular Function:
uroporphyrinogen-III synthase activity
Directly Involved In:
uroporphyrinogen III biosynthetic process
Supporting Evidence:
  • file:PSEPK/hemD/hemD-uniprot.txt
    Catalyzes cyclization of the linear tetrapyrrole,

References

Loading supporting content…

Download this section (compressed HTML)

Suggested Questions for Experts

Q: Does the hemC-hemD neighborhood support transcriptional coupling in KT2440?

Suggested Experiments

Experiment: Measure uroporphyrinogen isomers after hemD depletion and genetic complementation under controlled oxygen conditions.

Hypothesis: HemD is the principal uroporphyrinogen-III synthase in KT2440.

Deep Research

OpenScientist

(hemD-deep-research-openscientist.md)

Loading supporting content…

Download this section (compressed HTML)

📚 Additional Documentation

Notes

(hemD-notes.md)

Loading supporting content…

Download this section (compressed HTML)

📄 View Raw YAML

Loading supporting content…

Download this section (compressed HTML)