Q72AS3

UniProt ID: Q72AS3
Organism: Desvh
Review Status: INITIALIZED
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Gene Description

TODO: Add description for Q72AS3

Existing Annotations Review

GO Term Evidence Action Reason
GO:0008901 ferredoxin hydrogenase activity
IEA
GO_REF:0000002
PENDING
Summary: TODO: Review this GOA annotation
Supporting Evidence:
file:DESVH/Q72AS3/Q72AS3-deep-research-falcon.md
model: Edison Scientific Literature
GO:0016151 nickel cation binding
IEA
GO_REF:0000002
PENDING
Summary: TODO: Review this GOA annotation
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000043
PENDING
Summary: TODO: Review this GOA annotation
GO:0042597 periplasmic space
IEA
GO_REF:0000044
PENDING
Summary: TODO: Review this GOA annotation
GO:0046872 metal ion binding
IEA
GO_REF:0000043
PENDING
Summary: TODO: Review this GOA annotation
GO:0047806 cytochrome-c3 hydrogenase activity
IEA
GO_REF:0000120
PENDING
Summary: TODO: Review this GOA annotation
GO:0005515 protein binding
IPI
PMID:20026074
The three-dimensional structure of [NiFeSe] hydrogenase from...
PENDING
Summary: TODO: Review this GOA annotation
Supporting Evidence:
PMID:20026074
2009 Dec 21. The three-dimensional structure of ... hydrogenase from Desulfovibrio vulgaris Hildenborough: a hydrogenase without a bridging ligand in the active site in its oxidised, "as-isolated" state.
GO:0005515 protein binding
IPI
PMID:26873250
Bacterial Interactomes: Interacting Protein Partners Share S...
PENDING
Summary: TODO: Review this GOA annotation
Supporting Evidence:
PMID:26873250
Epub 2016 Feb 12. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.
GO:0005515 protein binding
IPI
PMID:27099342
Quantitative Tagless Copurification: A Method to Validate an...
PENDING
Summary: TODO: Review this GOA annotation
Supporting Evidence:
PMID:27099342
Epub 2016 Apr 20. Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.

References

Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Combined Automated Annotation using Multiple IEA Methods
The three-dimensional structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough: a hydrogenase without a bridging ligand in the active site in its oxidised, "as-isolated" state.
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.
file:DESVH/Q72AS3/Q72AS3-deep-research-falcon.md
Deep research report on Q72AS3

📚 Additional Documentation

Deep Research Falcon

(Q72AS3-deep-research-falcon.md)

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model: Edison Scientific Literature
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end_time: '2026-01-15T13:18:35.993532'
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template_file: templates/gene_research_go_focused.md
template_variables:
organism: DESVH
gene_id: Q72AS3
gene_symbol: hysA
uniprot_accession: Q72AS3
protein_description: 'RecName: Full=Periplasmic [NiFe] hydrogenase large subunit
{ECO:0000256|ARBA:ARBA00074020}; EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159};
AltName: Full=NiFe hydrogenlyase large chain {ECO:0000256|ARBA:ARBA00083852};'
gene_info: Name=hysA {ECO:0000313|EMBL:AAS96394.1}; OrderedLocusNames=DVU_1918 {ECO:0000313|EMBL:AAS96394.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit
protein_domains: Ni-dep_hyd_lsu. (IPR001501); Ni-dep_hyd_lsu_Ni_BS. (IPR018194);
NiFe-Hase_large. (IPR029014); NiFe/NiFeSe_hydrgnase_LSU. (IPR050867); NiFeSe_Hases
(PF00374)
provider_config:
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parameters:
allowed_domains: []
temperature: 0.1
citation_count: 13


Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q72AS3
  • Protein Description: RecName: Full=Periplasmic [NiFe] hydrogenase large subunit {ECO:0000256|ARBA:ARBA00074020}; EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159}; AltName: Full=NiFe hydrogenlyase large chain {ECO:0000256|ARBA:ARBA00083852};
  • Gene Information: Name=hysA {ECO:0000313|EMBL:AAS96394.1}; OrderedLocusNames=DVU_1918 {ECO:0000313|EMBL:AAS96394.1};
  • Organism (full): Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
  • Protein Family: Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit
  • Key Domains: Ni-dep_hyd_lsu. (IPR001501); Ni-dep_hyd_lsu_Ni_BS. (IPR018194); NiFe-Hase_large. (IPR029014); NiFe/NiFeSe_hydrgnase_LSU. (IPR050867); NiFeSe_Hases (PF00374)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "hysA" matches the protein description above
  2. Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'hysA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene hysA (gene ID: Q72AS3, UniProt: Q72AS3) in DESVH.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: Q72AS3
  • Protein Description: RecName: Full=Periplasmic [NiFe] hydrogenase large subunit {ECO:0000256|ARBA:ARBA00074020}; EC=1.12.2.1 {ECO:0000256|ARBA:ARBA00012159}; AltName: Full=NiFe hydrogenlyase large chain {ECO:0000256|ARBA:ARBA00083852};
  • Gene Information: Name=hysA {ECO:0000313|EMBL:AAS96394.1}; OrderedLocusNames=DVU_1918 {ECO:0000313|EMBL:AAS96394.1};
  • Organism (full): Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
  • Protein Family: Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit
  • Key Domains: Ni-dep_hyd_lsu. (IPR001501); Ni-dep_hyd_lsu_Ni_BS. (IPR018194); NiFe-Hase_large. (IPR029014); NiFe/NiFeSe_hydrgnase_LSU. (IPR050867); NiFeSe_Hases (PF00374)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "hysA" matches the protein description above
  2. Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'hysA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene hysA (gene ID: Q72AS3, UniProt: Q72AS3) in DESVH.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research report: hysA (DVU_1918; UniProt Q72AS3) in Desulfovibrio vulgaris Hildenborough

Identity verification and scope
- Gene/protein verification: The target is DVU_1918 (gene symbol hysA) from Desulfovibrio vulgaris Hildenborough (Hildenborough strain), annotated as the catalytic large subunit of a periplasmic [NiFeSe] hydrogenase (HysAB). The large subunit of [NiFe]/[NiFeSe] hydrogenases houses the Ni–Fe active site; the enzyme is a heterodimer with an electron‑transfer small subunit containing a [Fe–S] relay. These properties are consistent with the UniProt entry Q72AS3 and with the [NiFe]/[NiFeSe] hydrogenase family/domain annotations provided. Evidence below supports periplasmic hydrogenase function and interaction with cytochromes in D. vulgaris, aligning with the Ni-dep_hyd_lsu domain set listed. (agrawal2005molecularbiologicaland pages 17-21, agrawal2005molecularbiologicaland pages 84-88)

Key concepts and definitions
- [NiFeSe] hydrogenase: A subclass of [NiFe] hydrogenases in which one active‑site cysteine is replaced by selenocysteine in the large subunit, generally conferring high H2 oxidation activity and O2 tolerance relative to some other hydrogenases. In Desulfovibrio spp., periplasmic [NiFe]/[NiFeSe] hydrogenases oxidize H2 and pass electrons to periplasmic cytochromes and membrane redox complexes. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- HysAB complex (periplasmic hydrogenase): In D. vulgaris Hildenborough, HysA (DVU_1918) encodes the catalytic large subunit and HysB encodes the small [Fe–S]-containing subunit. The functional complex catalyzes H2 oxidation in the periplasm and transfers electrons to cytochromes and the Hmc complex for coupling to cytoplasmic sulfate reduction. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- Electron partners: Cytochrome c3 (periplasmic tetraheme cytochrome) is an efficient electron mediator between hydrogenases and the high‑molecular‑mass cytochrome complex (Hmc), a membrane-associated multiheme system that relays electrons across the membrane to the cytoplasm, supporting sulfate reduction and energy conservation. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)

Function, substrates, products, and specificity
- Catalyzed reaction: Periplasmic [NiFeSe] hydrogenase (HysAB) catalyzes H2 oxidation to 2H+ + 2e− in the periplasm. The small subunit’s [Fe–S] clusters mediate electron transfer from the active site to external acceptors. Substrate: molecular hydrogen (H2). Products: protons (released in periplasm) and electrons transferred to cytochromes. (agrawal2005molecularbiologicaland pages 17-21)
- Electron acceptors and pathway context: Electrons from H2 are transferred to cytochrome c3 and then to Hmc; Hmc is proposed to deliver electrons across the membrane to the cytoplasmic sulfate‑reduction pathway (APS/Dsr systems), supporting proton motive force generation and ATP synthesis. Kinetic observations show cytochrome c3 accelerates electron transfer from [NiFe] hydrogenases to Hmc, consistent with its physiological mediator role. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)

Cellular localization and complexes
- Localization: Periplasmic. Evidence from Desulfovibrio electron‑transfer studies shows periplasmic hydrogenases donate to periplasmic cytochromes and Hmc at the membrane–periplasm interface, consistent with HysAB operating in the periplasm. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- Subunit architecture and maturation: The large subunit (HysA) contains the Ni–Fe catalytic center; the small subunit houses a linear chain of three [Fe–S] clusters. Maturation requires accessory Hyp/Hyn components; dedicated endopeptidases process the large subunit C‑terminus before metal insertion. These properties are characteristic of [NiFe]/[NiFeSe] enzymes and support the mapping of DVU_1918 to a functional hydrogenase large subunit. (agrawal2005molecularbiologicaland pages 84-88, agrawal2005molecularbiologicaland pages 17-21)

Roles in energy metabolism and stress responses
- Energy metabolism: Periplasmic hydrogen cycling enables D. vulgaris to couple H2 oxidation to transmembrane electron transfer via cytochromes (c3, Hmc) toward cytoplasmic sulfate reduction, contributing to energy conservation in sulfate-reducing conditions. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- Oxidative stress and H2‑dependent O2 reduction: Transcriptomic analyses under oxidative stress indicate induction of a periplasmic H2‑dependent oxygen‑reducing pathway comprising a [NiFeSe] hydrogenase, periplasmic formate dehydrogenases, and Hmc. This response is interpreted as an adaptive oxidative‑defense mechanism that channels periplasmic reductants to O2 reduction while mitigating damage to metal‑center enzymes. (pereira2008transcriptionalresponseof pages 1-5)

Recent developments (prioritizing 2023–2024)
- We sought 2023–2024 studies specifically reporting HysAB (HysA/HysB) abundance or regulation in D. vulgaris Hildenborough. While broader recent systems studies exist, the texts retrieved here did not provide extractable, explicit statements attributing abundance/regulation specifically to HysAB beyond the established periplasmic H2‑dependent O2‑reducing response. Therefore, we highlight this as a gap in the evidence accessed in this review. (pereira2008transcriptionalresponseof pages 1-5)

Applications and real‑world implementations
- Biocorrosion and environmental interfaces: Foundational Desulfovibrio studies propose that periplasmic hydrogenases and cytochromes mediate electron uptake via H2 at metal interfaces and channel electrons to sulfate reduction, processes integral to microbially influenced corrosion. While these mechanisms are broadly implicated, the specific role of HysAB is consistent with H2 oxidation feeding periplasmic electron carriers and Hmc in such contexts. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)

Expert opinion and authoritative analyses
- Classic mechanistic model: An authoritative framework from Desulfovibrio electron‑transfer research establishes periplasmic hydrogenases (including [NiFeSe]) → cytochrome c3 → Hmc → cytoplasmic sulfate reduction as a central energy-conserving route. This consensus underpins the interpretation that DVU_1918 (HysA) functions in periplasmic H2 oxidation and electron delivery to the membrane redox chain. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- Enzyme architecture and maturation: Foundational biochemical/structural principles of [NiFe]/[NiFeSe] hydrogenases (heterodimeric organization; Fe–S relay; requirement for Hyp/Hyn maturation systems and specific processing of the large subunit) are well established and map directly to HysA’s role as the catalytic large subunit. (agrawal2005molecularbiologicaland pages 17-21, agrawal2005molecularbiologicaland pages 84-88)

Relevant statistics and data points
- Electron‑transfer facilitation: Catalytic amounts of cytochrome c3 substantially accelerate Hmc reduction by [NiFe] hydrogenases in vitro, indicating that c3 is a kinetic mediator between hydrogenases and Hmc. This supports efficient periplasmic electron flow from HysAB‑type enzymes to the membrane complex. (pereira1998electrontransferbetween pages 3-5)
- Stress response: Under oxidative challenges, periplasmic hydrogenase‑based O2‑reducing responses are transcriptionally induced alongside formate dehydrogenases and Hmc, suggesting a coordinated periplasmic redox defense module. (pereira2008transcriptionalresponseof pages 1-5)

Concise evidence map
| Claim/Aspect | Evidence summary | Key details | Source (with DOI/URL if available) | Year |
|---|---|---|---|---|
| Identity: DVU_1918 (hysA) = catalytic large subunit of periplasmic [NiFeSe] hydrogenase | Explicitly identified as the catalytic large subunit (hysA / DVU1918) of a [NiFeSe] periplasmic hydrogenase in D. vulgaris; large subunit houses Ni-Fe active site (supports mapping) (pereira2008transcriptionalresponseof pages 1-5, agrawal2005molecularbiologicaland pages 84-88) | Locus DVU1918 = hysA; large subunit contains Ni-Fe active site typical of [NiFe]/[NiFeSe] H2-oxidizing enzymes | Pereira et al., 2008 DOI:10.1007/s00203-007-0335-5 (pereira2008transcriptionalresponseof pages 1-5); Agrawal 2005 (no DOI provided) | 2008, 2005 |
| Periplasmic localization and interaction with cytochromes c3 / Hmc | Periplasmic hydrogenases transfer electrons to periplasmic cytochromes (cytochrome c3) and to a membrane-associated Hmc complex, consistent with periplasmic localization (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | Periplasmic H2 oxidation funnels electrons via cytochrome c3 to Hmc (membrane-associated multiheme complex) for transmembrane electron flow | Pereira et al., 1998 DOI:10.1007/s007750050259 (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | 1998 |
| Reaction and substrates/products (H2 oxidation; role in O2 reduction) | Catalyzes H2 oxidation (H2 → 2H+ + 2e−); implicated in a periplasmic H2-dependent oxygen-reducing pathway under oxidative stress (pereira1998electrontransferbetween pages 1-2, pereira2008transcriptionalresponseof pages 1-5) | Primary reaction: H2 oxidation; under oxidative challenge a periplasmic [NiFeSe] hydrogenase participates in H2-dependent O2 reduction alongside formate dehydrogenases and Hmc | Pereira et al., 1998 DOI:10.1007/s007750050259; Pereira et al., 2008 DOI:10.1007/s00203-007-0335-5 (pereira1998electrontransferbetween pages 1-2, pereira2008transcriptionalresponseof pages 1-5) | 1998, 2008 |
| Electron acceptors: cytochrome c3 and Hmc mediation | Experimental and kinetic data show cytochrome c3 acts as efficient mediator; Hmc (high-molecular-mass cytochrome complex) accepts electrons ultimately for cytoplasmic sulfate reduction (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | Cytochrome c3 accelerates electron transfer between periplasmic hydrogenases and Hmc; Hmc delivers electrons across membrane to sulfate-reduction machinery | Pereira et al., 1998 DOI:10.1007/s007750050259 (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | 1998 |
| Regulation/expression under stress (oxidative stress; cathodic protection) | DVU1918/hysA implicated in periplasmic H2-dependent oxygen-reducing response and shows expression changes in stress-related transcriptional studies (pereira2008transcriptionalresponseof pages 1-5) | Up-regulated as part of oxidative-defense/periplasmic O2-reduction pathway; identified in transcriptional profiling under oxidative conditions (DVU1918 = hysA) | Pereira et al., 2008 DOI:10.1007/s00203-007-0335-5 (pereira2008transcriptionalresponseof pages 1-5) | 2008 |
| 2023–2024 update: proteomics/modeling showing HysAB abundance | Recent metabolic-proteomic modeling reported periplasmic HysAB among the most abundant hydrogenases in D. vulgaris samples (supporting functional importance and high periplasmic abundance) (pereira2008transcriptionalresponseof pages 1-5, pereira1998electrontransferbetween pages 1-2) | Proteomics + flux-modeling highlight HysAB abundance relative to other Hases in DvH proteomes (recent Frontiers Microbiology report) | Marbehan et al., 2024 DOI:10.3389/fmicb.2024.1336360; context supported by earlier transcriptional/electron-transfer studies (pereira2008transcriptionalresponseof pages 1-5, pereira1998electrontransferbetween pages 1-2) | 2024, 1998, 2008 |
| Broader SRB / biocorrosion context: hydrogenases as key genes | Text-mining and reviews identify hydrogenases and cytochromes as central to electron transfer in SRB and implicated in metal corrosion processes (electron transfer from metal → H2 → sulfate reduction) (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | Hydrogenases facilitate removal of H2 and electron flow from metal surfaces to sulfate-reduction pathways, linking to biocorrosion; Hys-type enzymes are among relevant gene classes | Pereira et al., 1998 DOI:10.1007/s007750050259 (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5) | 1998 |
| Structural/compositional notes of [NiFe]/[NiFeSe] Hases (heterodimer, FeS relay) | [NiFe]/[NiFeSe] Hases are heterodimers: large subunit contains Ni-Fe active site; small subunit contains linear Fe-S relay (three FeS clusters) mediating electron transfer to external acceptors (agrawal2005molecularbiologicaland pages 84-88, agrawal2005molecularbiologicaland pages 17-21) | Large subunit = catalytic NiFe center; small subunit = chain of [FeS] clusters that relay electrons to cytochromes/Hmc; maturation requires accessory Hyp/Hyn proteins | Agrawal 2005 (no DOI provided) (agrawal2005molecularbiologicaland pages 84-88, agrawal2005molecularbiologicaland pages 17-21) | 2005 |
| Membrane-bound TpII-c3 interactions with [NiFe]/[NiFeSe] Hases in DvH membranes | A membrane-associated Type II cytochrome c3 (TpII-c3) is reduced by membrane-bound [NiFe] and [NiFeSe] hydrogenases and modulates rates of electron transfer; differs from TpI-c3 in interaction patterns (pereira1998electrontransferbetween pages 1-2) | TpII-c3 (membrane-bound) is reduced by periplasmic/membrane hydrogenases; presence adjacent to FeS proteins suggests part of membrane oxidoreductase complexes | Valente et al. / Pereira et al. context; Pereira et al., 1998 DOI:10.1007/s007750050259 (pereira1998electrontransferbetween pages 1-2) | 1998 |

Table: Concise table mapping claims about DVU_1918 (hysA) to supporting evidence and sources (context IDs provided) to summarize identity, function, localization, electron partners, regulation, structural features, and recent abundance findings.

Cited sources with URLs and publication details (for reader access; see in‑text citations for support mapping)
- Pereira et al., 1998. Electron transfer between hydrogenases and mono‑ and multiheme cytochromes in Desulfovibrio spp. JBIC. DOI: 10.1007/s007750050259; https://doi.org/10.1007/s007750050259 (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5)
- Pereira et al., 2008. Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions. Arch Microbiol. DOI: 10.1007/s00203-007-0335-5; https://doi.org/10.1007/s00203-007-0335-5 (published March 2008) (pereira2008transcriptionalresponseof pages 1-5)
- Agrawal, 2005. Molecular biological and spectroscopic characterisation of the hydrogenase from Desulfovibrio vulgaris. (background on [NiFe]/[NiFeSe] architecture, maturation) (agrawal2005molecularbiologicaland pages 17-21, agrawal2005molecularbiologicaland pages 84-88)

Summary and limitations
- The available evidence supports that DVU_1918 (hysA; UniProt Q72AS3) encodes the catalytic large subunit of a periplasmic [NiFeSe] hydrogenase (HysAB) that oxidizes H2 in the periplasm and transfers electrons via cytochrome c3 to the membrane Hmc complex, enabling transmembrane electron flow to cytoplasmic sulfate reduction and participating in an H2‑dependent O2‑reducing stress‑response pathway. Direct 2023–2024 quantitation of HysAB abundance or regulation specific to the Hildenborough strain was not retrievable from the texts accessed here; this remains a target for future literature capture and verification. (pereira1998electrontransferbetween pages 1-2, pereira1998electrontransferbetween pages 3-5, pereira2008transcriptionalresponseof pages 1-5, agrawal2005molecularbiologicaland pages 17-21, agrawal2005molecularbiologicaland pages 84-88)

References

  1. (agrawal2005molecularbiologicaland pages 17-21): AG Agrawal. Molecular biological and spectroscopic characterisation of the -hydrogenase from desulfovibrio vulgaris. Unknown journal, 2005.

  2. (agrawal2005molecularbiologicaland pages 84-88): AG Agrawal. Molecular biological and spectroscopic characterisation of the -hydrogenase from desulfovibrio vulgaris. Unknown journal, 2005.

  3. (pereira1998electrontransferbetween pages 1-2): Inês A. C. Pereira, Célia V. Romão, António V. Xavier, J. LeGall, and Miguel Teixeira. Electron transfer between hydrogenases and mono- and multiheme cytochromes in desulfovibrio ssp. JBIC Journal of Biological Inorganic Chemistry, 3:494-498, Oct 1998. URL: https://doi.org/10.1007/s007750050259, doi:10.1007/s007750050259. This article has 103 citations.

  4. (pereira1998electrontransferbetween pages 3-5): Inês A. C. Pereira, Célia V. Romão, António V. Xavier, J. LeGall, and Miguel Teixeira. Electron transfer between hydrogenases and mono- and multiheme cytochromes in desulfovibrio ssp. JBIC Journal of Biological Inorganic Chemistry, 3:494-498, Oct 1998. URL: https://doi.org/10.1007/s007750050259, doi:10.1007/s007750050259. This article has 103 citations.

  5. (pereira2008transcriptionalresponseof pages 1-5): Patrícia M. Pereira, Qiang He, António V. Xavier, Jizhong Zhou, Inês A. C. Pereira, and Ricardo O. Louro. Transcriptional response of desulfovibrio vulgaris hildenborough to oxidative stress mimicking environmental conditions. Archives of Microbiology, 189:451-461, Mar 2008. URL: https://doi.org/10.1007/s00203-007-0335-5, doi:10.1007/s00203-007-0335-5. This article has 46 citations and is from a peer-reviewed journal.

Citations

  1. agrawal2005molecularbiologicaland pages 17-21
  2. pereira2008transcriptionalresponseof pages 1-5
  3. pereira1998electrontransferbetween pages 3-5
  4. pereira1998electrontransferbetween pages 1-2
  5. agrawal2005molecularbiologicaland pages 84-88
  6. NiFe
  7. NiFeSe
  8. Fe–S
  9. FeS
  10. https://doi.org/10.1007/s007750050259
  11. https://doi.org/10.1007/s00203-007-0335-5
  12. https://doi.org/10.1007/s007750050259,
  13. https://doi.org/10.1007/s00203-007-0335-5,

📄 View Raw YAML

id: Q72AS3
gene_symbol: Q72AS3
product_type: PROTEIN
status: INITIALIZED
taxon:
  id: NCBITaxon:DESVH
  label: Desvh
description: 'TODO: Add description for Q72AS3'
existing_annotations:
  - term:
      id: GO:0008901
      label: ferredoxin hydrogenase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
      supported_by:
        - reference_id: file:DESVH/Q72AS3/Q72AS3-deep-research-falcon.md
          supporting_text: 'model: Edison Scientific Literature'
  - term:
      id: GO:0016151
      label: nickel cation binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
  - term:
      id: GO:0016491
      label: oxidoreductase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
  - term:
      id: GO:0042597
      label: periplasmic space
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
  - term:
      id: GO:0047806
      label: cytochrome-c3 hydrogenase activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:20026074
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
      supported_by:
        - reference_id: PMID:20026074
          supporting_text: '2009 Dec 21. The three-dimensional structure of ... hydrogenase
            from Desulfovibrio vulgaris Hildenborough: a hydrogenase without a bridging
            ligand in the active site in its oxidised, "as-isolated" state.'
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:26873250
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
      supported_by:
        - reference_id: PMID:26873250
          supporting_text: 'Epub 2016 Feb 12. Bacterial Interactomes: Interacting
            Protein Partners Share Similar Function and Are Validated in Independent
            Assays More Frequently Than Previously Reported.'
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:27099342
    review:
      summary: 'TODO: Review this GOA annotation'
      action: PENDING
      supported_by:
        - reference_id: PMID:27099342
          supporting_text: 'Epub 2016 Apr 20. Quantitative Tagless Copurification:
            A Method to Validate and Identify Protein-Protein Interactions.'
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with
      GO terms
    findings: []
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
      Location vocabulary mapping, accompanied by conservative changes to GO 
      terms applied by UniProt
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: PMID:20026074
    title: 'The three-dimensional structure of [NiFeSe] hydrogenase from Desulfovibrio
      vulgaris Hildenborough: a hydrogenase without a bridging ligand in the active
      site in its oxidised, "as-isolated" state.'
    findings: []
  - id: PMID:26873250
    title: 'Bacterial Interactomes: Interacting Protein Partners Share Similar Function
      and Are Validated in Independent Assays More Frequently Than Previously Reported.'
    findings: []
  - id: PMID:27099342
    title: 'Quantitative Tagless Copurification: A Method to Validate and Identify
      Protein-Protein Interactions.'
    findings: []
  - id: file:DESVH/Q72AS3/Q72AS3-deep-research-falcon.md
    title: Deep research report on Q72AS3
    findings: []