Periplasmic [NiFe] hydrogenase large subunit (hynA1/DVU_1922) catalyzing H2 oxidation with cytochrome c3 as the physiological electron acceptor. This enzyme is part of the hydrogen-cycling machinery that couples periplasmic H2 oxidation to dissimilatory sulfate reduction in D. vulgaris Hildenborough. The large subunit contains the bimetallic [NiFe] active site with CO and CN ligands on Fe, while the small subunit (HynB) provides the Fe-S cluster relay for electron transfer to cytochrome c3. The heterodimer is exported to the periplasm via the Tat pathway, with the small subunit carrying the twin-arginine signal peptide.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008901 ferredoxin hydrogenase activity | IEA GO_REF:0000002 | MODIFY | Summary: This annotation assigns ferredoxin hydrogenase activity based on InterPro domain matching (IPR018194). However, the physiological electron acceptor for this periplasmic [NiFe] hydrogenase is cytochrome c3, not ferredoxin. The GO term GO:0008901 describes the reaction "2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2" which is the H2 evolution direction with ferredoxin as electron donor - opposite to the physiological function of this uptake hydrogenase. Deep research summaries indicate that periplasmic [NiFe] hydrogenases in Desulfovibrio transfer electrons primarily to tetraheme cytochrome c3. Reason: The annotation is based on domain similarity but assigns an incorrect electron partner (ferredoxin) and incorrect reaction direction (H2 production vs uptake). D. vulgaris Hildenborough periplasmic [NiFe] hydrogenases function as H2 uptake enzymes with cytochrome c3 as the immediate acceptor. "Periplasmic electron transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171)" as summarized in the deep research report. The more appropriate term is GO:0047806 (cytochrome-c3 hydrogenase activity) which describes the correct reaction with the physiological acceptor. Proposed replacements: cytochrome-c3 hydrogenase activity Supporting Evidence: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md Electron acceptors and redox partners: Periplasmic electron transfer proceeds primarily to tetraheme cytochrome c3 (TpIc3; DVU3171) at high cellular abundance, which can mediate rapid electron transfer to the high-molecular-mass cytochrome (Hmc) transmembrane complex |
| GO:0016151 nickel cation binding | IEA GO_REF:0000002 | ACCEPT | Summary: This annotation correctly identifies nickel binding based on InterPro domain matching for the [NiFe] hydrogenase large subunit (IPR001501, IPR018194). The large subunit contains the bimetallic [NiFe] active site where Ni is coordinated by conserved cysteine residues. UniProt annotation shows Ni(2+) binding sites at positions 80, 83, and 545 of this protein. The [NiFe] center is essential for catalytic activity. Reason: [NiFe] hydrogenases are defined by their bimetallic active site containing nickel and iron. "The [NiFe] active sites contain a heterobimetallic Ni-Fe center with diatomic ligands (CO and CN-) on Fe" (deep research). UniProt structural annotation confirms multiple Ni(2+) binding residues in this protein. This is a core functional property of all [NiFe] hydrogenases. Supporting Evidence: UniProt:Q72AS0 BINDING 80 /ligand="Ni(2+)" /ligand_id="ChEBI:CHEBI:49786" /evidence="ECO:0000256|PIRSR:PIRSR601501-1" |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000043 | ACCEPT | Summary: This is a generic annotation based on UniProt keyword mapping (KW-0560: Oxidoreductase). While technically correct - hydrogenases are oxidoreductases that catalyze H2 + A = 2H+ + AH2 - this term is too general and provides no specific information about the enzyme's function. More specific child terms are available and already annotated (GO:0047806 cytochrome-c3 hydrogenase activity). Reason: Although this term is very general, it is not incorrect. The enzyme is indeed an oxidoreductase (EC 1.12.2.1). Since more specific annotations exist (GO:0047806), this general term provides hierarchical coverage without being misleading. The presence of more specific terms means this annotation adds little information but also does no harm. Supporting Evidence: UniProt:Q72AS0 EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159} |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: This cellular component annotation correctly identifies periplasmic localization based on UniProt subcellular location vocabulary mapping. D. vulgaris Hildenborough possesses multiple periplasmic [NiFe] hydrogenases that oxidize H2 in the periplasm and transfer electrons to the periplasmic cytochrome c3 pool. The heterodimeric enzyme is exported to the periplasm via the Tat (twin-arginine translocase) pathway. Reason: Periplasmic localization is strongly supported by multiple lines of evidence. The genome analysis "showed multiple periplasmic NiFe hydrogenases" in D. vulgaris Hildenborough (deep research). The Tat export pathway for periplasmic hydrogenases is summarized in the deep research report. UniProt annotation states "Periplasm {ECO:0000256|ARBA:ARBA00004418}". Supporting Evidence: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md Localization: The periplasm is the site of H2 oxidation in DvH; periplasmic [NiFe] hydrogenases deliver electrons into the periplasmic cytochrome network. Genome analysis explicitly highlighted multiple periplasmic NiFe hydrogenases initiating energy transduction. UniProt:Q72AS0 SUBCELLULAR LOCATION: Periplasm {ECO:0000256|ARBA:ARBA00004418} |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: This generic annotation for metal ion binding is derived from UniProt keyword mapping (KW-0479: Metal-binding). While technically accurate - the enzyme binds Ni, Fe, and Mg - this term is too general. More specific metal binding terms (GO:0016151 nickel cation binding) are already annotated and more informative. Reason: The annotation is correct but redundant given the more specific GO:0016151 (nickel cation binding) annotation. The protein does bind multiple metal ions (Ni, Fe, Mg) at the active site and structural positions. UniProt shows binding sites for Ni(2+), Fe cation, and Mg(2+). While not maximally informative, this general annotation is not misleading. Supporting Evidence: UniProt:Q72AS0 Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|PIRSR:PIRSR601501-1}; Nickel {ECO:0000256|ARBA:ARBA00022596, ECO:0000256|PIRSR:PIRSR601501-1}; |
| GO:0047806 cytochrome-c3 hydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the most accurate molecular function annotation for this enzyme. GO:0047806 describes "Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3" which matches the physiological function of periplasmic [NiFe] hydrogenases in Desulfovibrio species. The annotation is derived from RHEA:20625 and EC:1.12.2.1. Kinetic studies demonstrated that cytochrome c3 is the primary physiological acceptor for periplasmic hydrogenases. Reason: This annotation captures the core molecular function of the enzyme. "Kinetic measurements in Desulfovibrio spp. show that the [NiFe] periplasmic hydrogenases reduce Hmc efficiently and that cytochrome c3 markedly accelerates Hmc reduction, positioning c3 as the principal immediate acceptor from hydrogenases" (Pereira et al. 1998). UniProt catalytic activity annotation confirms: "2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 H(+)". EC 1.12.2.1 (hydrogen:cytochrome-c3 oxidoreductase) is the assigned enzyme classification. Supporting Evidence: UniProt:Q72AS0 EC=1.12.2.1; Evidence={ECO:0000256|ARBA:ARBA00029307}; file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md Biochemical/electrochemical analyses in Desulfovibrio emphasize cytochrome c3 as the principal physiological partner for periplasmic hydrogenases, accelerating electron delivery to transmembrane complexes like Hmc |
| GO:0019420 dissimilatory sulfate reduction | NAS file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md | NEW | Summary: This biological process annotation captures the pathway context in which hynA1 functions. The periplasmic [NiFe] hydrogenases provide electrons from H2 oxidation that feed into the cytoplasmic sulfate reduction pathway via membrane-spanning complexes. While hynA1 does not directly catalyze sulfate reduction, it is part of the electron transport chain that powers this process. Reason: The role of periplasmic [NiFe] hydrogenases in dissimilatory sulfate reduction is well established. "Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic sulfate reduction" (deep research). This represents the core biological role of this enzyme in D. vulgaris energy metabolism. GO annotation guidelines support annotating enzymes to the biological process they contribute to even when they don't directly catalyze the terminal reaction. Supporting Evidence: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md Central role in sulfate respiration: Periplasmic H2 oxidation via [NiFe] hydrogenases provides electrons to the periplasmic cytochrome pool and inner-membrane complexes, coupling to cytoplasmic sulfate reduction and contributing to proton motive force via periplasmic proton release. |
| GO:0019645 anaerobic electron transport chain | NAS file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md | NEW | Summary: The periplasmic [NiFe] hydrogenase operates as part of the anaerobic electron transport chain in D. vulgaris, transferring electrons from H2 to cytochrome c3 and onward to membrane complexes (Hmc/Tmc) that link to cytoplasmic terminal reductases. Reason: D. vulgaris is an obligate anaerobe and its periplasmic hydrogenases function in the context of anaerobic respiration. "Electrons are captured by tetraheme cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic H2 oxidation to cytoplasmic sulfate reduction" (deep research). This accurately describes participation in an anaerobic electron transport chain. Supporting Evidence: file:DESVH/Q72AS0/Q72AS0-deep-research-falcon.md In the hydrogen-cycling model, H2 produced (or supplied) is oxidized in the periplasm; electrons are captured by tetraheme cytochrome c3 and relayed to inner-membrane redox complexes (e.g., Hmc/Tmc modules), linking periplasmic H2 oxidation to cytoplasmic sulfate reduction and proton motive force generation. |
Loading supporting content…
Download this section (compressed HTML)Q: What is the relative contribution of hynA1 vs the [NiFeSe] hydrogenase to H2 uptake under different growth conditions?
Q: Does hynA1 have any role in hydrogen production under certain physiological conditions?
Q: What is the kinetic preference of hynA1 for different cytochrome c3 isoforms?
Experiment: Deletion mutant phenotyping under H2/sulfate growth to quantify contribution to sulfate reduction
Hypothesis: hynA1 is required for efficient H2-dependent sulfate reduction under specific growth conditions.
Experiment: Comparative kinetic analysis with purified enzyme and different cytochrome acceptors
Hypothesis: HynA1 preferentially transfers electrons to specific cytochrome c3 isoforms.
Experiment: Expression analysis under syntrophic growth conditions
Hypothesis: hynA1 expression is upregulated during syntrophic growth where H2 is limiting.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)