| Feature | APS Reductase (AprA) | Succinate Dehydrogenase (SdhA) | Diagnostic? |
|---|---|---|---|
| FAD binding mode | Non-covalent FAD cofactor bound in AprA active site; reduced FAD N5 attacks APS sulfur (pqac-00000007, pqac-00000011, pqac-00000013) | Covalently bound FAD via 8α-N3-histidyl linkage in SDHA/SdhA (pqac-00000015, pqac-00000016) | **Yes** |
| FAD attachment residue | No covalent attachment residue; FAD held non-covalently by AprA matrix (pqac-00000011, pqac-00000013) | His-99 in human SDHA; equivalent histidine is the covalent flavin ligand in bacterial homologs (pqac-00000015, pqac-00000016) | **Yes** |
| Substrate | Adenosine 5'-phosphosulfate (APS) (pqac-00000008, pqac-00000010) | Succinate / dicarboxylate substrate (pqac-00000016) | **Yes** |
| Product(s) | Sulfite + AMP in APS reduction (pqac-00000008, pqac-00000010) | Fumarate + reduced electron acceptor in succinate oxidation (pqac-00000016) | **Yes** |
| Catalytic mechanism | Nucleophilic attack of reduced FAD N5 on APS sulfur, forming FAD-APS and FAD-sulfite intermediates (pqac-00000007, pqac-00000010, pqac-00000011) | Dicarboxylate chemistry at complex II active site; succinate/fumarate interconversion with flavin-dependent redox chemistry and distinct active-site geometry (pqac-00000015, pqac-00000016) | **Yes** |
| Key active-site residue 1 | Arg-A265 hydrogen-bonds to APS sulfate and helps activate substrate (pqac-00000010, pqac-00000013, pqac-00000014) | Arg-R340 binds dicarboxylate substrate in SDH active site (pqac-00000016) | Different |
| Key active-site residue 2 | His-A398 hydrogen-bonds to APS sulfate and supports catalysis (pqac-00000010, pqac-00000013, pqac-00000014) | His-H407 participates in SDH active-site network (pqac-00000016) | Different |
| Key active-site residue 3 | Asn-A74 shapes FAD re-face and stabilizes bent flavin conformation (pqac-00000011, pqac-00000013) | His-H296 contributes to dicarboxylate/flavinylation-active-site chemistry (pqac-00000016) | Different |
| Key active-site residue 4 | Trp-A234 shapes FAD re-face and bent isoalloxazine geometry (pqac-00000011, pqac-00000013) | Arg-R451 stabilizes catalytic intermediate and is critical for flavinylation-competent SDH conformation (pqac-00000016) | Different |
| Iron-sulfur clusters | Two [4Fe-4S] clusters in AprB beta subunit (pqac-00000008, pqac-00000007) | Distinct complex II Fe-S relay in SdhB/Ip subunit, not the AprB two-[4Fe-4S] arrangement (pqac-00000016) | Different arrangement |
| Complex subunit composition | AprA-AprB heterodimeric iron-sulfur flavoenzyme (1:1 alpha/beta) (pqac-00000008, pqac-00000007) | SdhABCD / complex II membrane-anchored heterotetramer (pqac-00000015, pqac-00000016) | Different |
| Cellular localization | Cytoplasmic or cytoplasmic face-associated sulfate-reduction enzyme linked to QmoABC (pqac-00000008, pqac-00000021, pqac-00000022) | Membrane-associated respiratory complex II (pqac-00000015, pqac-00000016) | Different |
| Metabolic pathway | Dissimilatory sulfate reduction / APS reduction pathway (pqac-00000008, pqac-00000021, pqac-00000022) | TCA cycle / oxidative phosphorylation / complex II respiration (pqac-00000015, pqac-00000016) | Different |
| GO term (correct) | GO:0033748 adenylylsulfate reductase activity (supported by AprA-specific mechanism and pathway context) (pqac-00000008, pqac-00000010, pqac-00000021) | GO:0000104 succinate dehydrogenase activity (appropriate for SDHA/SdhA, not AprA) (pqac-00000015, pqac-00000016) | Different branches |
| Domain architecture | FAD-binding domain + capping domain + helical domain; overall classified in fumarate reductase family fold (pqac-00000007, pqac-00000008) | Related flavoprotein fold with FAD-binding/capping architecture in complex II flavoprotein (pqac-00000015, pqac-00000016) | Shared fold, different function |
| Covalent FAD attachment factor | None reported/required for AprA non-covalent FAD loading (pqac-00000007, pqac-00000011) | Requires SdhE/SDHAF2-type assembly factor for covalent flavinylation (pqac-00000015, pqac-00000016) | **Yes** |


*Table: This table contrasts the catalytic machinery, cofactors, subunit organization, and pathway context of APS reductase AprA and succinate dehydrogenase SdhA. It shows that the proteins share a broad fold family but belong to different functional subfamilies, explaining why the propagated GO:0000104 annotation is a within-superfamily misplacement.*