| Citation | Evidence Type | Supports/Refutes/Qualifies | Claim Tested | Key Finding | Organism/Assay Context | Confidence and Limitations |
|---|---|---|---|---|---|---|
| Meyer & Kuever 2008, *PLoS ONE* 3:e1514, doi:10.1371/journal.pone.0001514 | Structural/evolutionary; homology modeling | Refutes | Q72DT2 AprA has succinate dehydrogenase activity | AprA is structurally in the fumarate reductase family, but its catalytic center is APS-reductase-specific: conserved AprA residues include Asn-A74, Trp-A234, Arg-A265, and His-A398; the mechanism is nucleophilic attack of reduced FAD N5 on APS sulfur, not succinate oxidation. D. vulgaris AprA model clusters with sulfate-reducing Apr enzymes, not SDH enzymes. (pqac-00000008, pqac-00000007, pqac-00000010, pqac-00000011, pqac-00000013, pqac-00000014) | Comparative models based on *Archaeoglobus fulgidus* AprBA templates; includes *D. vulgaris* AprA/AprB models | High for family placement and active-site interpretation; indirect for Q72DT2 because modeled from homologous structures rather than direct biochemical assay of this exact protein |
| Meyer & Kuever 2007, *Microbiology* 153:3478-3498, doi:10.1099/mic.0.2007/008250-0 | Phylogenetic/evolutionary | Refutes | AprA is a succinate dehydrogenase-family enzyme in function rather than only in fold | The paper explicitly states that only AprA has structural similarity to succinate-dehydrogenase/fumarate-reductase flavoproteins, but this relationship is **not reflected in sequence similarity**; aprBA phylogeny and locus context identify the protein specifically as dissimilatory APS reductase. (pqac-00000005, pqac-00000006) | Broad phylogeny of aprBA genes across sulfur oxidizers and sulfate reducers | High for distinguishing structural analogy from true functional orthology; not a direct activity assay |
| Ramos et al. 2012, *Frontiers in Microbiology* 3:137, doi:10.3389/fmicb.2012.00137 | Direct biochemical interaction; mutant phenotype | Supports | AprA participates in the APS-reduction/sulfate-reduction pathway in *D. vulgaris* | QmoABC interacts directly with AprAB with strong affinity (KD = 90 ± 3 nM); qmoABC is essential for growth on sulfate but not sulfite/thiosulfate, placing AprAB in the APS reduction step of sulfate respiration rather than TCA/respiratory complex II succinate oxidation. (pqac-00000021, pqac-00000022, pqac-00000023) | *Desulfovibrio* spp.; co-immunoprecipitation, cross-linking, Far-Western, tag-affinity purification, SPR, growth phenotypes | High for pathway assignment; does not directly assay AprA catalysis or exclude every remote moonlighting activity, but strongly supports APS-reductase role |
| Fritz et al. 2002, *PNAS* 99:1836-1841, doi:10.1073/pnas.042664399 | Structural biology; crystal structure | Refutes | AprA catalytic chemistry matches succinate dehydrogenase | Crystal structure of APS reductase shows an APS-reductase active center with non-covalently bound FAD and key active-site residues including Arg-A265 and His-A398; this chemistry is for APS reduction/sulfite oxidation, not succinate/fumarate interconversion. (pqac-00000007, pqac-00000010, pqac-00000011, pqac-00000013, pqac-00000014) | *Archaeoglobus fulgidus* APS reductase crystal structure used as template for bacterial AprA interpretation | High for mechanistic distinction at the subfamily level; limitation is that it is a homologous enzyme, not the exact *D. vulgaris* protein |
| Sharma et al. 2020, *PNAS* 117:23548-23556, doi:10.1073/pnas.2007391117 | Structural/mechanistic comparison | Refutes | AprA could directly have SDH catalytic machinery | SDH/complex II uses a distinct catalytic architecture: covalent FAD linkage via His-H99 and active-site residues H296, T308, R340, H407, and R451. These defining SDH features differ fundamentally from AprA, whose FAD is non-covalent and whose catalytic residues are different. (pqac-00000015, pqac-00000016) | Human SDHA-SDHAF2 assembly intermediate; interpreted against bacterial complex II literature | High for defining canonical SDH chemistry; limitation is species difference, but active-site logic is broadly conserved across SDH homologs |
| Trotter et al. 2023, *Frontiers in Microbiology* 14:1095191, doi:10.3389/fmicb.2023.1095191 | Genome-wide genetics; fitness profiling | Supports | aprA is required for sulfate-based physiology in *D. vulgaris* | Large-scale transposon analysis identifies a robust essential gene set in *D. vulgaris* under sulfate-rich growth; the study independently describes APS reductase as a key enzyme whose futile substrate interaction explains molybdate toxicity, consistent with aprA functioning in sulfate reduction rather than as SDH. (pqac-00000017, pqac-00000018, pqac-00000019) | *D. vulgaris Hildenborough* RB-TnSeq / Tn-seq fitness assays across 757 experiments | Moderate to high for pathway importance; limitation is that the provided excerpts do not explicitly name aprA in the essentiality paragraph, so inference is supported by study context rather than a quoted aprA fitness value |
| Bramlett & Peck 1975, *Journal of Biological Chemistry* 250:2979-2986, doi:10.1016/S0021-9258(19)41583-4 | Direct enzyme assay; biochemical characterization | Supports | Q72DT2 encodes adenylylsulfate reductase rather than SDH | Historical direct biochemical characterization reported kinetic properties of adenylyl sulfate reductase from *D. vulgaris*, providing primary experimental support that the enzyme in this organism catalyzes APS reduction. (pqac-00000020) | *D. vulgaris* enzyme purification and kinetic analysis | Moderate: highly relevant primary assay, but full text/details were not available in the retrieved context, so specific kinetic constants could not be verified here |
| Kushkevych 2016/2020 reviews, doi:10.30970/sbi.1001.560 and doi:10.3390/cells9030698 | Review/database synthesis | Supports/Qualifies | Community consensus on AprAB function in *Desulfovibrio* | Reviews consistently describe AprAB as the key APS reductase in dissimilatory sulfate reduction in *Desulfovibrio*, matching the genomic and biochemical literature and opposing an SDH annotation. (pqac-00000003) | Review summaries of sulfate-reduction pathways in intestinal and environmental sulfate-reducing bacteria | Moderate: useful corroboration and current consensus, but not primary evidence; should not be used alone for curation |
| Cross-evidence synthesis from AprA-vs-SDH active-site comparisons | Comparative mechanistic inference | Refutes | The TreeGrafter propagation failed only in granularity, not function | The decisive error is **within-superfamily mis-placement**: AprA and SDHA share a fold family, but differ in substrate class, cofactor attachment mode, catalytic residues, pathway context, and gene neighborhood. The annotation is not merely too broad; it names the wrong sibling activity. (pqac-00000005, pqac-00000007, pqac-00000010, pqac-00000015, pqac-00000016, pqac-00000021) | Integrated inference from structural, phylogenetic, biochemical, and genetic evidence | High for curation conclusion; limitation is that this is a synthesis row rather than a single experiment |


*Table: This table summarizes the key evidence bearing on whether Q72DT2 (aprA) from *Desulfovibrio vulgaris* directly has succinate dehydrogenase activity. The matrix shows that the annotation is best explained as a within-superfamily mis-placement: AprA is an APS reductase, not a succinate dehydrogenase.*