APS-dependent assimilatory sulfate reduction

A reusable pathway that converts sulfate to sulfide through adenosine 5'-phosphosulfate (APS) and sulfite. The module contains sulfate activation by ATP sulfurylase, thioredoxin-dependent APS reduction, and assimilatory sulfite reduction. It represents the direct APS branch rather than the alternative APS-kinase/PAPS-reductase route. Sulfate import is upstream, whereas siroheme synthesis and incorporation of sulfide into cysteine are supporting or downstream biology outside the pathway boundary.

MODULE:aps_dependent_assimilatory_sulfate_reductionDRAFTMetabolic Pathwaymodules/aps_dependent_assimilatory_sulfate_reduction.yaml
sulfate assimilationGO:0000103
GO:0000103
sulfate assimilation
GO:0000103 provides the biological-process context.
RHEA:18133
sulfate adenylyltransferase reaction
RHEA:18133 defines ATP-dependent formation of APS from sulfate.
RHEA:21976
adenylyl-sulfate reductase reaction
RHEA:21976 defines the reversible thioredoxin-dependent APS/sulfite reaction catalyzed physiologically toward sulfite during assimilation.
GO:0050311
sulfite reductase (ferredoxin) activity
GO:0050311 captures the ferredoxin-fed sulfite-reductase implementation supported as the current Pseudomonas model.
PANTHER:PTHR32439
ferredoxin sulfite/nitrite reductase family
This broad siroheme-reductase family contains characterized ferredoxin-dependent sulfite reductases such as UniProtKB:P9WJ02 and distinguishes that implementation from the PTHR11493 classical CysI family when combined with the required molecular function.
GO:0004783
sulfite reductase (NADPH) activity
GO:0004783 captures the classical CysJ/CysI NADPH-dependent bacterial implementation.
PMID:16387658
Molecular basis for G protein control of the prokaryotic ATP sulfurylase.
Biochemistry and structure establish the proteobacterial CysD/CysN complex and energetic coupling of CysN GTP turnover to APS formation.
PMID:23794620
Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads.
Pseudomonas genetics support an FprA-fed CysI sulfite-reduction system distinct from enterobacterial CysJ/CysI.
file:projects/P_PUTIDA/deep-research/PSEPK__aps_dependent_assimilatory_sulfate_reduction__ppu00920-deep-research-openscientist.md
OpenScientist PSEPK ppu00920 satisfiability review
The species-aware review evaluates whether the curated PSEPK genes satisfy this module within the wider sulfur-metabolism map.
file:PSEPK/cysD/cysD-ai-review.yaml
PSEPK cysD gene review
Q88NA9 supplies the ATP sulfurylase catalytic subunit.
file:PSEPK/cysNC/cysNC-ai-review.yaml
PSEPK cysNC gene review
Q88NA8 supplies the ATP sulfurylase regulatory GTPase subunit.
file:PSEPK/cysH/cysH-ai-review.yaml
PSEPK cysH gene review
Q88KG2 supplies the APS-to-sulfite reaction.
file:PSEPK/cysI/cysI-ai-review.yaml
PSEPK cysI gene review
Q88KB9 supplies the sulfite-reductase catalytic hemoprotein.
file:PSEPK/fpr-I/fpr-I-ai-review.yaml
PSEPK fpr-I gene review
Q88MD5 supplies the FprA-type electron-transfer role.
6Nodes
3Parts
1Variant Sets
2Variants
5Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:aps_dependent_assimilatory_sulfate_reduction 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.

Gene-review completeness (5/10 grounded genes reviewed)

4 complete review(s) · 2 with deep research · 5 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
cysD Q88NA9 ✓ ✓ ✗
cysH Q88KG2 ✓ ✓ ✓
cysI Q88KB9 ✓ ✓ ✓
cysNC Q88NA8 ✓ ✓ ✗
fpr-I Q88MD5 ✓ 3/5 ✗
Escherichia coli K-12 CysI P17846 ✗ — —
Escherichia coli K-12 CysD P21156 ✗ — —
Escherichia coli K-12 CysN P23845 ✗ — —
Escherichia coli K-12 CysJ P38038 ✗ — —
Mycobacterium tuberculosis Sir P9WJ02 ✗ — —

Details

APS-dependent assimilatory sulfate reductionMetabolic Pathwayaps_dependent_assimilatory_sulfate_reduction
sulfate assimilationGO:0000103

This module deliberately represents the direct APS-reduction route. An APS-kinase/PAPS-reductase branch should be modeled as a separate route variant rather than adding a PAPS step to every instance. Exact UniProt exemplars delimit the CysD/CysN, ferredoxin/Fpr, and CysJ/CysI implementations without restricting the module taxonomically. No molecular function or location is duplicated at module level, and no ancestral PTN node is asserted without verified PAINT IBD evidence.

Connections

ATP sulfurylase supplies APS to CysH.
CysH supplies sulfite to the terminal sulfite-reduction system.
Part 1: sulfate activation
Sulfate activation to APSReactionsulfate_activation_step

Annotons

CysD/CysN ATP sulfurylase
cysdn_atp_sulfurylase
Participant: Protein Complex: proteobacterial CysD/CysN ATP sulfurylase
Protein Complex:
proteobacterial CysD/CysN ATP sulfurylase Heteromeric sulfate adenylyltransferase with a CysD nucleotidyltransferase subunit and a regulatory CysN GTPase.
Active units:
CysD sulfate adenylyltransferase subunit 2
Participant: Family: CysD sulfate adenylyltransferase subunit 2 family
Family:
CysD sulfate adenylyltransferase subunit 2 familyPANTHER:PTHR43196:SF1
Representative Members: PSEPK CysDUniProtKB:Q88NA9 Escherichia coli K-12 CysDUniProtKB:P21156
Role: Catalytic ATP-utilizing sulfate-adenylation subunit.
Function:
sulfate adenylyltransferase (ATP) activityGO:0004781
CysN regulatory GTPase subunit
Participant: Family: CysN sulfate adenylyltransferase regulatory subunits
Family:
CysN sulfate adenylyltransferase regulatory subunitsInterPro:IPR011779
Representative Members: PSEPK CysNCUniProtKB:Q88NA8 Escherichia coli K-12 CysNUniProtKB:P23845
Role: Couples GTP hydrolysis to APS formation by CysD.
Function:
GTPase activityGO:0003924

Function

sulfate adenylyltransferase (ATP) activityGO:0004781
Substrates: sulfate ATP proton
Products: adenosine 5'-phosphosulfate diphosphate

Forms APS as the activated sulfate intermediate.

Part 2: APS reduction
APS reduction to sulfiteReactionaps_reduction_step

Annotons

Thioredoxin-dependent APS reductase
cysH_aps_reductase
Participant: Family: CysH APS reductases
Family:
CysH APS reductasesInterPro:IPR011798
Representative Members: PSEPK CysHUniProtKB:Q88KG2

Function

adenylyl-sulfate reductase (thioredoxin) activityGO:0043866
Substrates: adenosine 5'-phosphosulfate reduced thioredoxin
Products: sulfite AMP oxidized thioredoxin

Reduces APS directly to sulfite without a PAPS intermediate.

Part 3: sulfite reduction
Assimilatory reduction of sulfite to sulfideReactionsulfite_reduction_step
Variant set: Sulfite-reductase electron-donor architecture by immediate electron-transfer system (Exactly One)

The catalytic siroheme/iron-sulfur hemoprotein is conserved, but lineages differ in whether electrons arrive through a separate CysJ flavoprotein or a ferredoxin/Fpr system.

Ferredoxin/Fpr-fed CysI routeReactionferredoxin_fpr_cysi_route

A CysI-family sulfite reductase receives reducing equivalents from reduced ferredoxin or directly from a type-1 Fpr enzyme. This architecture occurs in bacterial systems that lack the classical CysJ diflavin partner.

Annotons

Ferredoxin-dependent CysI activity
ferredoxin_dependent_cysi_activity
Participant: Family: ferredoxin sulfite/nitrite reductase family
Family:
ferredoxin sulfite/nitrite reductase familyPANTHER:PTHR32439
Representative Members: PSEPK CysIUniProtKB:Q88KB9 Mycobacterium tuberculosis SirUniProtKB:P9WJ02
Required Function:
sulfite reductase (ferredoxin) activityGO:0050311
PTHR32439 is broader than sulfite reductases and the Q88KB9 subfamily label is not functionally reliable. The required function and characterized P9WJ02 exemplar delimit this selector; the classical CysJ/CysI branch instead uses PTHR11493:SF47.

Function

sulfite reductase (ferredoxin) activityGO:0050311
Substrates: sulfite reduced ferredoxin
Products: sulfide oxidized ferredoxin water

Performs the six-electron reduction of sulfite.

Fpr electron supply
fpr_electron_supply
Participant: Family: bacterial type-1 ferredoxin--NADP reductases
Family:
bacterial type-1 ferredoxin--NADP reductasesPANTHER:PTHR47878:SF1
Representative Members: PSEPK Fpr-IUniProtKB:Q88MD5

Function

ferredoxin-NADP+ reductase activityGO:0004324

Supplies reducing equivalents to the CysI system through ferredoxin or direct electron transfer.

CysJ/CysI NADPH-dependent routeReactioncysji_nadph_route

The classical enterobacterial implementation uses a CysJ diflavin subunit to transfer electrons from NADPH to the CysI siroheme/iron-sulfur catalytic subunit.

Annotons

CysJ/CysI NADPH sulfite reductase
cysji_nadph_sulfite_reductase
Participant: Protein Complex: CysJ/CysI sulfite reductase complex
Protein Complex:
CysJ/CysI sulfite reductase complexGO:0009337
Active units:
CysJ flavoprotein electron-transfer subunit
Participant: Family: CysJ NADPH sulfite-reductase flavoproteins
Family:
CysJ NADPH sulfite-reductase flavoproteinsPANTHER:PTHR19384:SF128
Representative Members: Escherichia coli K-12 CysJUniProtKB:P38038
Role: Transfers electrons from NADPH to CysI.
CysI hemoprotein catalytic subunit
Participant: Family: NADPH-dependent CysI hemoproteins
Family:
NADPH-dependent CysI hemoproteinsPANTHER:PTHR11493:SF47
Representative Members: Escherichia coli K-12 CysIUniProtKB:P17846
Role: Reduces sulfite at the siroheme/iron-sulfur center.

Function

sulfite reductase (NADPH) activityGO:0004783
Substrates: sulfite NADPH proton
Products: sulfide NADP+ water

Performs NADPH-dependent reduction of sulfite to sulfide.