Siroheme biosynthesis from uroporphyrinogen III

Biosynthesis of siroheme, the iron-containing isobacteriochlorin prosthetic group of assimilatory sulfite and nitrite reductases, from the common tetrapyrrole precursor uroporphyrinogen III. Three reactions are required: S-adenosyl-L-methionine-dependent bis-methylation of uroporphyrinogen III at C-2 and C-7 to precorrin-2, NAD(P)+-dependent dehydrogenation of precorrin-2 to sirohydrochlorin, and insertion of ferrous iron into sirohydrochlorin to give siroheme. The chemistry is conserved in bacteria, fungi and plants, but the enzyme architecture differs. In enterobacteria a single multifunctional siroheme synthase (CysG) carries all three activities, with the methylase in its C-terminal region and the dehydrogenase and chelatase sharing an N-terminal region. Fungi split the pathway between a monofunctional uroporphyrinogen-III methyltransferase (Met1-type) and a bifunctional dehydrogenase-ferrochelatase (Met8-type) that uses a single active site for both reactions. Bacillus and plants use separate enzymes for every step, including a small SirB-type sirohydrochlorin ferrochelatase that in plants is located in the plastid. Uroporphyrinogen III synthesis is shared with heme, chlorophyll and cobalamin biosynthesis and lies upstream of this module; incorporation of siroheme into sulfite reductase lies downstream.

MODULE:siroheme_biosynthesisDRAFTMetabolic Pathwaymodules/siroheme_biosynthesis.yaml
siroheme biosynthetic processGO:0019354
YeastPathways:PWY-5194-1
siroheme biosynthesis (S. cerevisiae, SGD YeastPathways)
Source pathway with three reactions: RXN-13403 (bis-methylation, MET1), DIMETHUROPORDEHYDROG-RXN (precorrin-2 dehydrogenase, MET8) and SIROHEME-FERROCHELAT-RXN (sirohydrochlorin ferrochelatase, MET8). All three catalyst assignments were retained after review; no enzyme is missing. The pathway comment notes that S. cerevisiae has no assimilatory nitrite reductase, so siroheme is used only by sulfite reductase in this yeast.
GO:0019354
siroheme biosynthetic process
Module-level biological process.
GO:0004851
uroporphyrin-III C-methyltransferase activity
Molecular function of the first (bis-methylation) step.
GO:0043115
precorrin-2 dehydrogenase activity
Molecular function of the second (dehydrogenation) step.
GO:0051266
sirohydrochlorin ferrochelatase activity
Molecular function of the terminal (iron insertion) step.
PMID:9003798
Siroheme biosynthesis in Saccharomyces cerevisiae requires the products of both the MET1 and MET8 genes.
Genetic identification of MET1 (identical to MET20) and MET8 as the S. cerevisiae siroheme biosynthesis genes.
The MET1 gene from S. cerevisiae was cloned and shown to be the same gene as MET20. Sequence similitudes as well as complementation studies indicate that Met1p and Met8p are both involved in siroheme biosynthesis.
PMID:10051442
The role of Saccharomyces cerevisiae Met1p and Met8p in sirohaem and cobalamin biosynthesis.
Complementation of cysG mutants and in vitro assay establish Met1p as the SAM-dependent uroporphyrinogen III methyltransferase and Met8p as the precorrin-2 dehydrogenase and sirohydrochlorin ferrochelatase.
MET1 encodes the S-adenosyl-l-methionine uroporphyrinogen III transmethylase activity, and MET8 encodes the dehydrogenase and chelatase activities (all three functions are encoded by Sal. typhimurium and E. coli cysG).
PMID:11980703
The structure of Saccharomyces cerevisiae Met8p, a bifunctional dehydrogenase and ferrochelatase.
Met8p carries out both terminal reactions with a single active site and a fold unrelated to other chelatases.
Analysis of mutant proteins suggests that both catalytic activities share a single active site, and that Asp141 plays an essential role in both dehydrogenase and chelatase processes.
PMID:8243665
The Escherichia coli cysG gene encodes the multifunctional protein, siroheme synthase.
E. coli CysG alone converts uroporphyrinogen III to siroheme.
Thus CysG is a multifunctional protein solely responsible for siroheme synthesis from uro'gen III in E. coli, and accordingly is renamed siroheme synthase.
PMID:7945210
Gene dissection demonstrates that the Escherichia coli cysG gene encodes a multifunctional protein.
The C-terminal region of CysG (residues 202-457) is the methyltransferase; the N-terminal region is required for the dehydrogenation and iron insertion steps.
The evidence presented in this paper suggests that the CysG protein is a multifunctional protein involved in SAM-dependent methylation, pyridine dinucleotide dependent dehydrogenation and ferrochelation.
PMID:12408752
Identification and functional analysis of enzymes required for precorrin-2 dehydrogenation and metal ion insertion in the biosynthesis of sirohaem and cobalamin in Bacillus megaterium.
Bacillus megaterium uses three separate enzymes, SirA, SirC (precorrin-2 dehydrogenase) and SirB (sirohydrochlorin ferrochelatase).
SirC was found to act as a precorrin-2 dehydrogenase, generating sirohydrochlorin, and SirB was found to act as a ferrochelatase responsible for the final step in sirohaem synthesis.
PMID:15545265
Identification and characterization of the terminal enzyme of siroheme biosynthesis from Arabidopsis thaliana: a plastid-located sirohydrochlorin ferrochelatase containing a 2FE-2S center.
Arabidopsis SirB is a small, chloroplast-located sirohydrochlorin ferrochelatase with an Fe-S centre.
Green fluorescent protein tagging revealed that it is located in the chloroplast.
PMID:1479340
Physiological analysis of mutants of Saccharomyces cerevisiae impaired in sulphate assimilation.
MET1 and MET8 are among the genes required for an enzymatically active sulfite reductase, linking this module to sulfate assimilation.
the products of at least five genes are needed for the synthesis of an enzymically active sulphite reductase. These genes are MET1, MET5, MET8, MET10 and MET20.
6Nodes
2Parts
1Variant Sets
3Variants
7Annotons
4Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:siroheme_biosynthesis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • uroporphyrinogen_methylation_step → dehydrogenation_ferrochelation_steps [NOT_CHECKED]

Function consistency and core coverage

3 gene-function check(s) reflected in core functions · 0 conflict(s) · 8 evidence or coverage gap(s) (17 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
sumt_activity MET1 (Saccharomyces cerevisiae)
UniProtKB:P36150
Family Representative 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sumt_activity CysG (Escherichia coli K-12)
UniProtKB:P0AEA8
Family Representative 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sumt_activity UPM1 (Arabidopsis thaliana)
UniProtKB:Q42606
Family Representative 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
met8_precorrin2_dehydrogenase MET8 (Saccharomyces cerevisiae)
UniProtKB:P15807
Family Representative 		precorrin-2 dehydrogenase activity
GO:0043115 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
met8_sirohydrochlorin_ferrochelatase MET8 (Saccharomyces cerevisiae)
UniProtKB:P15807
Family Representative 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
cysg_precorrin2_dehydrogenase CysG (Escherichia coli K-12)
UniProtKB:P0AEA8
Gene 		precorrin-2 dehydrogenase activity
GO:0043115 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
cysg_sirohydrochlorin_ferrochelatase CysG (Escherichia coli K-12)
UniProtKB:P0AEA8
Gene 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sirc_precorrin2_dehydrogenase SirC (Bacillus megaterium)
UniProtKB:P61818
Family Representative 		precorrin-2 dehydrogenase activity
GO:0043115 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sirb_sirohydrochlorin_ferrochelatase SirB (Bacillus megaterium)
UniProtKB:P61817
Family Representative 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sirb_sirohydrochlorin_ferrochelatase SIRB (Arabidopsis thaliana)
UniProtKB:Q84JH7
Family Representative 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
sumt_activity siroheme synthase-related tetrapyrrole methyltransferase family
PANTHER:PTHR45790:SF6
Family 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Family Supported
Family review supports GO:0004851 for PANTHER:PTHR45790:SF6. Asserted by siroheme_biosynthesis; accepted by MET1. CysG (SF1) and plant UPM1 (SF3) carry it too.
sumt_activity siroheme synthase-related tetrapyrrole methyltransferase family
PANTHER:PTHR45790:SF1
Family 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Family Supported
Family review supports GO:0004851 for PANTHER:PTHR45790:SF1. Asserted by siroheme_biosynthesis; accepted by MET1. CysG (SF1) and plant UPM1 (SF3) carry it too.
sumt_activity siroheme synthase-related tetrapyrrole methyltransferase family
PANTHER:PTHR45790:SF3
Family 		uroporphyrin-III C-methyltransferase activity
GO:0004851 		Family Supported
Family review supports GO:0004851 for PANTHER:PTHR45790:SF3. Asserted by siroheme_biosynthesis; accepted by MET1. CysG (SF1) and plant UPM1 (SF3) carry it too.
met8_precorrin2_dehydrogenase Met8-type bifunctional siroheme synthesis proteins
PANTHER:PTHR35330
Family 		precorrin-2 dehydrogenase activity
GO:0043115 		Family Supported
Family review supports GO:0043115 FAMILY_WIDE. Asserted by siroheme_biosynthesis for MET8 and SirC; accepted by MET8.
met8_sirohydrochlorin_ferrochelatase Met8-type bifunctional siroheme synthesis proteins
PANTHER:PTHR35330:SF1
Family 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Family Supported
Family review supports GO:0051266 for PANTHER:PTHR35330:SF1. Chelatase activity of bifunctional Met8 (SF1); monofunctional SirC lacks it.
sirc_precorrin2_dehydrogenase SirC/Met8-type precorrin-2 dehydrogenases
PANTHER:PTHR35330
Family 		precorrin-2 dehydrogenase activity
GO:0043115 		Family Supported
Family review supports GO:0043115 FAMILY_WIDE. Asserted by siroheme_biosynthesis for MET8 and SirC; accepted by MET8.
sirb_sirohydrochlorin_ferrochelatase SirB-type sirohydrochlorin ferrochelatases
PANTHER:PTHR33542
Family 		sirohydrochlorin ferrochelatase activity
GO:0051266 		Family Function Unreviewed
Family review leaves GO:0051266 UNRESOLVED. Asserted by siroheme_biosynthesis for SirB. The same subfamily contains CbiX cobaltochelatases, so ferrochelatase activity cannot be scoped by subfamily.

Gene-review completeness (2/7 grounded genes reviewed)

2 complete review(s) · 2 with deep research · 5 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
MET1 P36150 ✓ ✓ ✓
MET8 P15807 ✓ ✓ ✓
CysG (Escherichia coli K-12) P0AEA8 ✗ — —
SirB (Bacillus megaterium) P61817 ✗ — —
SirC (Bacillus megaterium) P61818 ✗ — —
UPM1 (Arabidopsis thaliana) Q42606 ✗ — —
SIRB (Arabidopsis thaliana) Q84JH7 ✗ — —

Details

Siroheme biosynthesis from uroporphyrinogen IIIMetabolic Pathwaysiroheme_biosynthesis
siroheme biosynthetic processGO:0019354

NEW module from YeastPathways PWY-5194-1 (2026-10). Boundary: starts at uroporphyrinogen III (shared with heme, chlorophyll and cobalamin; its synthesis by the HEM enzymes is upstream) and ends with free siroheme. Insertion of siroheme into sulfite reductase belongs to aps_dependent_assimilatory_sulfate_reduction, whose sulfite-reduction step depends on this module (in S. cerevisiae met1 and met8 mutants lack sulfite reductase activity, PMID:1479340); cobaltochelation of sirohydrochlorin for anaerobic cobalamin synthesis (CbiK/CbiX) is a separate branch. YeastCyc assessment - the three reactions and the MET1 and MET8 assignments are correct; YeastCyc's comment speaks of "four enzymatic steps" because the bis-methylation is two methyl transfers in one reaction (RXN-13403). Compartment: the yeast GO-CAM places all three activities in the cytosol, whereas plant SUMT and SirB are plastid enzymes, so no compartment is asserted at module level. Architecture is modelled as an explicit variant set for the two terminal reactions (bifunctional Met8, the N-terminal region of trifunctional CysG, or separate SirC + SirB); the methylase step is a single family role whose exemplars include the CysG C-terminal region. S. pombe orthologs (SPCC1739.06c SUMT and met8) exist but no PomBase GO-CAM is linked to this module, so they are not used as exemplars. GO-CAM comparison - YeastPathways_PWY-5194-1 agrees with the module on genes, functions and compartment, but has no causal edges between the three activities. In GOA, MET8 also carries an IDA for GO:0004325 protoporphyrin ferrochelatase activity (PMID:11980703); the physiologically relevant substrate is sirohydrochlorin and only GO:0051266 is used here.

Connections

SUMT supplies precorrin-2 to the dehydrogenase.
Part 1: SAM-dependent bis-methylation of uroporphyrinogen III
Uroporphyrinogen III to precorrin-2Reactionuroporphyrinogen_methylation_step

Annotons

Uroporphyrinogen-III C-methyltransferase (SUMT)
sumt_activity
Participant: Family: siroheme synthase-related tetrapyrrole methyltransferase family
Family:
siroheme synthase-related tetrapyrrole methyltransferase family
Representative Members: MET1 (Saccharomyces cerevisiae)UniProtKB:P36150 CysG (Escherichia coli K-12)UniProtKB:P0AEA8 UPM1 (Arabidopsis thaliana)UniProtKB:Q42606
Required Function:
uroporphyrin-III C-methyltransferase activityGO:0004851
PTHR45790 also contains cobalamin-pathway uroporphyrinogen methyltransferases (CobA-type) that perform the same reaction; the required function, not the family, delimits the role.

Function

uroporphyrin-III C-methyltransferase activityGO:0004851
Substrates: uroporphyrinogen III S-adenosyl-L-methionine (2 equivalents)
Products: precorrin-2 S-adenosyl-L-homocysteine (2 equivalents)

Transfers two methyl groups from SAM to C-2 and C-7 of uroporphyrinogen III, committing it to the siroheme (and cobalamin) branch.

Part 2: precorrin-2 dehydrogenation and iron insertion
Precorrin-2 to siroheme (dehydrogenation then ferrochelation)Metabolic Pathwaydehydrogenation_ferrochelation_steps

Two consecutive reactions: NAD(P)+-dependent oxidation of precorrin-2 to sirohydrochlorin, then insertion of Fe2+ into sirohydrochlorin to give siroheme. Both are always required; the lineages differ in whether one bifunctional enzyme, one domain of a trifunctional siroheme synthase, or two separate enzymes catalyse them.

Variant set: Dehydrogenase/ferrochelatase enzyme architecture by enzyme architecture (Exactly One)

PANTHER PTHR35330:SF1 groups bifunctional Met8 with the monofunctional Bacillus precorrin-2 dehydrogenase SirC, so family membership does not establish chelatase activity; the required function on each participant delimits the role.

Bifunctional Met8-type dehydrogenase-ferrochelataseMetabolic Pathwaymet8_bifunctional_variant

Fungal architecture: one protein with a single active site performs both reactions (S. cerevisiae Met8p).

Annotons

Met8-type precorrin-2 dehydrogenase activity
met8_precorrin2_dehydrogenase
Participant: Family: Met8-type bifunctional siroheme synthesis proteins
Family:
Met8-type bifunctional siroheme synthesis proteinsPANTHER:PTHR35330
Representative Members: MET8 (Saccharomyces cerevisiae)UniProtKB:P15807
Required Function:
precorrin-2 dehydrogenase activityGO:0043115

Function

precorrin-2 dehydrogenase activityGO:0043115
Substrates: precorrin-2 NAD+
Products: sirohydrochlorin NADH

Oxidises precorrin-2 to sirohydrochlorin.

Met8-type sirohydrochlorin ferrochelatase activity
met8_sirohydrochlorin_ferrochelatase
Participant: Family: Met8-type bifunctional siroheme synthesis proteins
Family:
Met8-type bifunctional siroheme synthesis proteins
Representative Members: MET8 (Saccharomyces cerevisiae)UniProtKB:P15807
Required Function:
sirohydrochlorin ferrochelatase activityGO:0051266

Function

sirohydrochlorin ferrochelatase activityGO:0051266
Substrates: sirohydrochlorin Fe2+
Products: siroheme 2 H+

Inserts ferrous iron into sirohydrochlorin to form siroheme.

Connections

Trifunctional CysG siroheme synthase (N-terminal region)Metabolic Pathwaycysg_trifunctional_variant

Enterobacterial architecture: the N-terminal region of the multifunctional CysG, which also carries the SUMT activity of part 1, performs dehydrogenation and iron insertion.

Annotons

CysG precorrin-2 dehydrogenase activity
cysg_precorrin2_dehydrogenase
Participant: Gene Product: CysG (Escherichia coli K-12)
Gene Product:
CysG (Escherichia coli K-12)UniProtKB:P0AEA8

Function

precorrin-2 dehydrogenase activityGO:0043115
Substrates: precorrin-2 NAD+
Products: sirohydrochlorin NADH

N-terminal-region dehydrogenase of the trifunctional siroheme synthase (PMID:8243665, PMID:7945210).

CysG sirohydrochlorin ferrochelatase activity
cysg_sirohydrochlorin_ferrochelatase
Participant: Gene Product: CysG (Escherichia coli K-12)
Gene Product:
CysG (Escherichia coli K-12)UniProtKB:P0AEA8

Function

sirohydrochlorin ferrochelatase activityGO:0051266
Substrates: sirohydrochlorin Fe2+
Products: siroheme

N-terminal-region ferrochelatase of the trifunctional siroheme synthase.

Connections

Separate SirC dehydrogenase and SirB ferrochelataseMetabolic Pathwayseparate_sirc_sirb_variant

Architecture of Bacillus and plants: a monofunctional precorrin-2 dehydrogenase (SirC in Bacillus) and a small SirB-type sirohydrochlorin ferrochelatase, which in plants is plastid-located and carries a 2Fe-2S centre.

Annotons

SirC monofunctional precorrin-2 dehydrogenase
sirc_precorrin2_dehydrogenase
Participant: Family: SirC/Met8-type precorrin-2 dehydrogenases
Family:
SirC/Met8-type precorrin-2 dehydrogenasesPANTHER:PTHR35330
Representative Members: SirC (Bacillus megaterium)UniProtKB:P61818
Required Function:
precorrin-2 dehydrogenase activityGO:0043115
No plant precorrin-2 dehydrogenase is used as an exemplar here; the plant enzyme for this step is not grounded by the evidence cited in this module.

Function

precorrin-2 dehydrogenase activityGO:0043115
Substrates: precorrin-2 NAD+
Products: sirohydrochlorin NADH

Oxidises precorrin-2 to sirohydrochlorin.

SirB sirohydrochlorin ferrochelatase
sirb_sirohydrochlorin_ferrochelatase
Participant: Family: SirB-type sirohydrochlorin ferrochelatases
Family:
SirB-type sirohydrochlorin ferrochelatasesPANTHER:PTHR33542
Representative Members: SirB (Bacillus megaterium)UniProtKB:P61817 SIRB (Arabidopsis thaliana)UniProtKB:Q84JH7
Required Function:
sirohydrochlorin ferrochelatase activityGO:0051266

Function

sirohydrochlorin ferrochelatase activityGO:0051266
Substrates: sirohydrochlorin Fe2+
Products: siroheme

Inserts ferrous iron into sirohydrochlorin to form siroheme.

Connections