Small (beta) subunit of the periplasmic [NiFe] hydrogenase of Desulfovibrio desulfuricans ATCC 27774 (hydA, Ddes_1039). It is synthesised with a twin-arginine (Tat) signal peptide and exported to the periplasm, where it forms a soluble heterodimer with the catalytic large subunit. The small subunit carries the iron-sulfur relay of the enzyme, two [4Fe-4S] clusters and one [3Fe-4S] cluster, which conducts electrons between the bimetallic Ni-Fe active site of the large subunit and the external redox partner; the distal [4Fe-4S] cluster is the docking site for the physiological acceptor, the tetrahaem cytochrome c3. In sulfate-reducing bacteria this periplasmic H2-oxidising enzyme feeds electrons from molecular hydrogen into the periplasmic cytochrome pool and hence into anaerobic (sulfate) respiration.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0008901 ferredoxin hydrogenase activity | IEA GO_REF:0000002 | REMOVE | Summary: An InterPro2GO transfer from IPR001821 ([NiFe]-hydrogenase, small subunit) assigning the ferredoxin-linked hydrogenase reaction. GO:0008901 is defined as "Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2", the [FeFe]/ferredoxin chemistry (EC 1.12.7.2). This enzyme is a periplasmic cytochrome-c3-linked [NiFe] hydrogenase (EC 1.12.2.1) whose physiological acceptor is the tetrahaem cytochrome c3, not ferredoxin. Reason: This is a demonstrably wrong electronic mapping rather than a judgement call about granularity: the acceptor named by the term is not the acceptor of this enzyme, and the correct acceptor-specific term (GO:0047806) is already present on this gene product from the EC mapping. The underlying InterPro2GO line is recorded as a source defect; a family-level signature spanning [NiFe] hydrogenases with different acceptors would be better mapped to the acceptor-agnostic GO:0033748 hydrogenase (acceptor) activity. Supporting Evidence: PMID:11191224 its physiological partner, the tetrahaem cytochrome c3 from the same organism file:DESDA/hydA/hydA-uniprot.txt Reaction=2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 |
| GO:0009055 electron transfer activity | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter assigns electron transfer activity from the [NiFe]/[NiFeSe] hydrogenase small subunit family node. This is the small subunit's own molecular function: it binds two [4Fe-4S] clusters and one [3Fe-4S] cluster that form the electron relay from the Ni-Fe active site of the large subunit to the external acceptor, with the distal [4Fe-4S] cluster forming the docking interface with tetrahaem cytochrome c3. Reason: The claim is specific to this chain and is supported by the structure of this very enzyme, in which the cluster chain runs from the distal cluster (the cytochrome c3 docking site) up to the [NiFe] centre, and by the curated cofactor content of the entry. Electron transfer, not a merely structural role, is what this subunit does, so it is retained as the core molecular function. Supporting Evidence: PMID:11191224 an interaction between the haem IV region in tetrahaem cytochrome c3 with the distal [4Fe-4S] cluster file:DESDA/hydA/hydA-uniprot.txt Note=Binds 2 [4Fe-4S] clusters. |
| GO:0009061 anaerobic respiration | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter assigns anaerobic respiration from the [NiFe] hydrogenase small subunit family node. Desulfovibrio periplasmic [NiFe] hydrogenase oxidises H2 on the periplasmic face and passes the electrons to the tetrahaem cytochrome c3 pool, the entry point of the anaerobic (sulfate) respiratory chain of these strictly anaerobic sulfate reducers. Reason: The subunit performs part of the work of the process rather than merely being required for it: it conducts the electrons released by H2 oxidation to the periplasmic cytochrome acceptor, which is the respiratory electron transfer step. The term is at the right level of generality for what is established here; a more specific process (e.g. dissimilatory sulfate reduction) would assert a coupling that has not been tested for this particular hydrogenase in this strain. Supporting Evidence: PMID:11191224 This interaction should correspond to efficient electron transfer and be physiologically relevant, given the proximity of the two redox centres |
| GO:0009375 ferredoxin hydrogenase complex | IEA GO_REF:0000002 | MODIFY | Summary: A second InterPro2GO transfer from IPR001821, placing the subunit in a ferredoxin hydrogenase complex. The enzyme this subunit belongs to is a [NiFe] heterodimer whose acceptor is cytochrome c3, and GO:0009375 sits under GO:0140535 intracellular protein-containing complex (confirmed in the GO ancestor closure over is_a and part_of), which is wrong for a Tat-exported periplasmic enzyme. Reason: The essence of the annotation, that this chain is part of a hydrogenase complex, is right; the particular complex named is not. The accurate term is GO:0044569 [Ni-Fe] hydrogenase complex, which this gene product already carries from TreeGrafter and which is accepted in this review. The mapping itself is recorded as a source defect against interpro2go. Proposed replacements: [Ni-Fe] hydrogenase complex Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt Heterodimer of a large and a small subunit. file:DESDA/hydA/hydA-uniprot.txt Predicted to be exported by the Tat system. The position of the |
| GO:0016020 membrane | IEA GO_REF:0000118 | REMOVE | Summary: TreeGrafter places the protein in a membrane from the family node. Many members of the [NiFe] hydrogenase small subunit family (for example the Escherichia coli Hyd-1 and Hyd-2 small subunits) carry a C-terminal membrane anchor, but this protein does not: it is a soluble periplasmic protein with a Tat signal peptide, no transmembrane segment in the record, and the holoenzyme from this strain was crystallised as a soluble periplasmic heterodimer. Reason: This is an over-propagated electronic annotation that can be argued against on the target's own evidence: the only hydrophobic segment of the precursor is the cleaved Tat signal, the mature chain begins at residue 50 and was isolated in soluble form for crystallography, and the curated subcellular location is the periplasmic space with no membrane component. Keeping the term would assert a membrane association for which there is no target-specific support. Propagation Review Root cause: PROPAGATION BAD Sources checked: PANTHER:PTN000768616 SUPPORTS SOURCE BUT NOT TARGET The family node is sound for the many membrane-anchored [NiFe] hydrogenase small subunits, but this member is a soluble Tat-exported periplasmic protein lacking the C-terminal anchor, so the location does not transfer. Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt SUBCELLULAR LOCATION: Periplasm. file:DESDA/hydA/hydA-uniprot.txt CHAIN 50..315 |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: Periplasmic localisation mapped from the curated UniProt subcellular location. The protein carries an experimentally confirmed twin-arginine (Tat) signal peptide whose cleavage position was determined by direct protein sequencing of the mature subunit, and the holoenzyme was purified and crystallised from this strain as a periplasmic enzyme. Reason: Localisation is supported independently of the automatic mapping: the mature N-terminus of the purified subunit begins after the Tat signal peptide (direct protein sequencing of residues 50-67), which establishes export across the cytoplasmic membrane, and Desulfovibrio periplasmic hydrogenases are the canonical periplasmic H2-oxidising enzymes of sulfate reducers. Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt SUBCELLULAR LOCATION: Periplasm. file:DESDA/hydA/hydA-uniprot.txt Predicted to be exported by the Tat system. The position of the |
| GO:0044569 [Ni-Fe] hydrogenase complex | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter places the subunit in the [Ni-Fe] hydrogenase complex. The enzyme is a heterodimer of this small subunit with the catalytic large subunit (UniProtKB:Q9L868 / Ddes_1038), and the heterodimer from this strain was solved crystallographically. Reason: This is the correct complex term for the chain and is directly supported: the large and small subunit genes are adjacent in the ATCC 27774 genome (Ddes_1038, Ddes_1039), the large subunit occupies chains B/D of PDB 1E3D, and the structure paper describes a single enzyme containing both the [NiFe] centre and the iron-sulfur cluster chain. Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt Heterodimer of a large and a small subunit. PMID:11191224 has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms |
| GO:0047806 cytochrome-c3 hydrogenase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: The EC/Rhea mapping assigns the holoenzyme reaction (2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 H+, EC 1.12.2.1) to this chain with an enables qualifier. The reaction is the right one for the enzyme, but H2 heterolysis happens at the bimetallic Ni-Fe site, which is carried entirely by the large subunit; the small subunit supplies the iron-sulfur relay that carries the electrons away to cytochrome c3. Reason: Following the subunit convention used elsewhere in this repository (for example PSEPK ureA, whose nickel active site resides in UreC), an individual non-catalytic chain should not be said to enable the holoenzyme activity. The annotation is not false about the enzyme, so it is kept rather than removed, and the relationship is recorded accurately in core_functions as contributes_to_molecular_function. The large subunit (UniProtKB:Q9L868) holds the Ni and Fe ligands and carries this activity in its own right. Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt Reaction=2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 PMID:11191224 a three-fold disorder was observed for Cys536 which binds to the nickel atom |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO assigns generic iron-sulfur cluster binding. The curated record states the actual cluster composition: two [4Fe-4S] clusters and one [3Fe-4S] cluster, with the coordinating cysteine residues annotated individually, so both specific child terms are supported. Reason: The term is correct but less specific than the evidence supports, so it is refined rather than kept. Both descendants are warranted and both are listed: GO:0051539 (4 iron, 4 sulfur cluster binding) for the two [4Fe-4S] clusters of the relay and GO:0051538 (3 iron, 4 sulfur cluster binding) for the [3Fe-4S] cluster. The structure of this enzyme resolves the clusters, including the modified [4Fe-3S-3O] proximal cluster. Proposed replacements: 4 iron, 4 sulfur cluster binding 3 iron, 4 sulfur cluster binding Supporting Evidence: file:DESDA/hydA/hydA-uniprot.txt Note=Binds 2 [4Fe-4S] clusters. file:DESDA/hydA/hydA-uniprot.txt Note=Binds 1 [3Fe-4S] cluster. PMID:11191224 has been modified [4Fe-3S-3O] by loss of one sulfur atom and inclusion of three oxygen atoms |
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Download this section (compressed HTML)Q: Does the ATCC 27774 periplasmic [NiFe] hydrogenase transfer electrons to acceptors other than the tetrahaem cytochrome c3 (for example the type II cytochrome c3 or the Hmc/Tmc transmembrane complexes), and with what kinetic preference?
Q: Is the H2-dependent reduction of soluble metal ions such as Pd(II) reported for whole Desulfovibrio cells catalysed at this enzyme, or is the enzyme only the source of low-potential electrons that reduce the metal non-enzymatically at the cell surface?
Experiment: Purify the heterodimer from ATCC 27774 and measure H2 oxidation with the tetrahaem cytochrome c3 and with alternative periplasmic cytochromes as acceptors, comparing steady-state rates and Km values.
Hypothesis: The tetrahaem cytochrome c3 is the kinetically preferred acceptor at the distal [4Fe-4S] cluster, as predicted by the docking study of the structure paper.
Experiment: Incubate the purified enzyme with Pd(II) under H2 in the presence and absence of cytochrome c3 and compare Pd(0) nanoparticle formation with that of enzyme-free and heat-inactivated controls.
Hypothesis: Pd(II) reduction requires catalytically competent enzyme rather than adventitious reduction by dissolved H2, and proceeds without the physiological acceptor.
Experiment: Construct a markerless deletion of the Ddes_1038-Ddes_1039 operon in ATCC 27774 and test H2-dependent Pd(II) and Tc(VII) reduction by resting cells against the wild type.
Hypothesis: The periplasmic [NiFe] hydrogenase is required for H2-dependent metal reduction at the cell surface, the inference that Lloyd et al. could not test genetically.
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