Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0016491 oxidoreductase activity	IEA GO_REF:0000120	ACCEPT	Summary: HdrA functions as the FAD-containing bifurcating subunit of the FlxABCD-HdrABC complex, mediating electron transfer between NADH, ferredoxin, and DsrC (Ferreira 2023). The term "oxidoreductase activity" is accurate but very general for a protein with such specific electron bifurcation function. Reason: The IEA annotation based on InterPro domain IPR023753 (FAD/NAD-binding domain) correctly identifies oxidoreductase activity. While this term is broad, it accurately captures the fundamental catalytic function. More specific terms for electron bifurcation activity do not yet exist in GO. The protein's FAD-dependent electron transfer function in the FlxABCD-HdrABC complex is well-documented (Ferreira 2023). Supporting Evidence: file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md HdrA contains six [4Fe–4S] clusters and one FAD file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit that organizes electron flow between a mid-potential pool (often NADH) and low-potential ferredoxin and/or protein disulfides
GO:0046872 metal ion binding	IEA GO_REF:0000043	ACCEPT	Summary: HdrA contains multiple iron-sulfur clusters that bind iron ions as part of their electron transfer function. The annotation is correct but less informative than the more specific iron-sulfur cluster binding terms. Reason: This IEA annotation based on UniProtKB keyword KW-0479 (Metal-binding) is correct. HdrA contains six [4Fe-4S] clusters that require iron binding (Ferreira 2023). While more specific annotations for 4Fe-4S cluster binding are also present, this general term is not incorrect and can be retained as it is encompassed by the more specific terms. Supporting Evidence: ferreira2023unravelingthemetabolic HdrA contains six [4Fe-4S] clusters and one FAD
GO:0051536 iron-sulfur cluster binding	IEA GO_REF:0000043	ACCEPT	Summary: HdrA contains multiple [4Fe-4S] clusters essential for its electron bifurcation function. Iron-sulfur cluster binding is a core molecular function of this protein. Reason: The IEA annotation based on UniProtKB keyword KW-0411 (Iron-sulfur) correctly identifies iron-sulfur cluster binding as a core function. HdrA contains six [4Fe-4S] clusters that mediate electron transfer in the bifurcating complex (Ferreira 2023). This annotation accurately reflects the protein's cofactor requirements. Supporting Evidence: ferreira2023unravelingthemetabolic HdrA contains six [4Fe-4S] clusters and one FAD ferreira2023unravelingthemetabolic conserved cofactor architecture (FAD; multiple [4Fe-4S] clusters)
GO:0051539 4 iron, 4 sulfur cluster binding	IEA GO_REF:0000043	ACCEPT	Summary: HdrA specifically contains six [4Fe-4S] clusters that are essential for intracomplex electron transfer during electron bifurcation/confurcation. Reason: This IEA annotation based on UniProtKB keyword KW-0004 (4Fe-4S) is highly accurate. The 2023 synthesis on D. vulgaris Hildenborough documents that HdrA contains six [4Fe-4S] clusters (Ferreira 2023). The UniProt entry also contains two annotated 4Fe-4S ferredoxin-type domains (positions 542-571 and 572-601). This is a core molecular function annotation. Supporting Evidence: ferreira2023unravelingthemetabolic HdrA contains six [4Fe-4S] clusters and one FAD ferreira2023unravelingthemetabolic Structural cofactor inventory: HdrA contains six [4Fe-4S] clusters and one FAD
GO:0005515 protein binding	IPI PMID:26873250 Bacterial Interactomes: Interacting Protein Partners Share S...	MODIFY	Summary: High-throughput AP-MS study in D. vulgaris identified interaction between Q72DT0 (HdrA/DVU_0849) and Q72DS8 (DVU_0851). Q72DS8 is likely HdrC or a Flx subunit based on genomic context. This interaction is biologically meaningful as HdrA functions within the FlxABCD-HdrABC complex. Reason: While the protein-protein interaction is experimentally validated (IPI evidence from AP-MS), the term "protein binding" (GO:0005515) is uninformative. HdrA physically interacts with other subunits of the FlxABCD-HdrABC complex as part of its electron bifurcation function. A more specific term would better capture the functional nature of this interaction. However, no more specific GO term adequately captures the interaction between electron bifurcating complex subunits. The interaction supports the complex formation but "protein binding" alone provides minimal functional insight. Proposed replacements: electron transfer activity Supporting Evidence: PMID:26873250 459 high confidence PPIs from D. vulgaris ferreira2023unravelingthemetabolic FlxABCD-HdrABC system: A composite enzyme system in D. vulgaris Hildenborough proposed to function as a novel NADH dehydrogenase/heterodisulfide reductase
GO:0005515 protein binding	IPI PMID:26873250 Bacterial Interactomes: Interacting Protein Partners Share S...	MODIFY	Summary: AP-MS study identified interaction between Q72DT0 (HdrA/DVU_0849) and Q72DT1 (DVU_0848). Q72DT1 is the adjacent gene product, likely HdrB based on operon organization. UniProt records 3 experiments supporting this interaction. Reason: The interaction with Q72DT1 (DVU_0848) is experimentally validated and biologically meaningful - this represents HdrA-HdrB interaction within the heterodisulfide reductase complex. However, "protein binding" is too generic. The HdrA-HdrB interaction is essential for the electron bifurcation mechanism, where HdrB contains additional [4Fe-4S] clusters that receive electrons from HdrA. Proposed replacements: electron transfer activity Supporting Evidence: PMID:26873250 459 high confidence PPIs from D. vulgaris ferreira2023unravelingthemetabolic HdrB contains two [4Fe-4S] clusters in the D. vulgaris Hildenborough system
GO:0005515 protein binding	IPI PMID:27099342 Quantitative Tagless Copurification: A Method to Validate an...	MODIFY	Summary: Independent validation of Q72DT0-Q72DS8 interaction via quantitative tagless copurification method. This study confirmed PPIs from the AP-MS interactome with high confidence. Reason: This represents independent experimental validation of the HdrA interaction with another complex subunit (Q72DS8/DVU_0851). The tagless copurification method provides orthogonal support for the AP-MS data. However, the annotation as "protein binding" remains uninformative for understanding the functional role of this interaction within the electron bifurcating complex. Proposed replacements: electron transfer activity Supporting Evidence: PMID:27099342 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome
GO:0005515 protein binding	IPI PMID:27099342 Quantitative Tagless Copurification: A Method to Validate an...	MODIFY	Summary: Independent validation of Q72DT0-Q72DT1 (HdrA-HdrB) interaction via quantitative tagless copurification. UniProt records 5 experiments total supporting this interaction. Reason: Strong experimental support from multiple independent methods confirms the HdrA-HdrB interaction. This is a core functional interaction within the FlxABCD-HdrABC complex. The generic "protein binding" term should be supplemented or replaced with more informative functional terms. Proposed replacements: electron transfer activity Supporting Evidence: PMID:27099342 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome ferreira2023unravelingthemetabolic HdrABC interacts directly with DsrC
GO:0050660 flavin adenine dinucleotide binding	IEA GO_REF:0000043	NEW	Summary: HdrA contains one FAD cofactor that is essential for its electron bifurcation function. FAD binding is a core molecular function. Reason: UniProt annotates FAD as a cofactor for this protein (ECO:0000256\|ARBA:ARBA00001974). The deep research confirms HdrA contains FAD which is central to flavin-based electron bifurcation mechanism. This annotation should be present but appears missing from the GOA file despite being in UniProt. Supporting Evidence: ferreira2023unravelingthemetabolic HdrA contains six [4Fe-4S] clusters and one FAD ferreira2023unravelingthemetabolic HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit
GO:0009055 electron transfer activity	ISS ferreira2023unravelingthemetabolic	NEW	Summary: HdrA functions as an electron transfer hub in the FlxABCD-HdrABC complex, mediating electron flow between NADH, ferredoxin, and DsrC. Reason: This is a core function of HdrA that is well-documented but not explicitly annotated. HdrA mediates electron transfer via its FAD and [4Fe-4S] clusters as part of flavin-based electron bifurcation. This annotation would more accurately capture the protein's primary molecular function than the current generic annotations. Supporting Evidence: ferreira2023unravelingthemetabolic HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit that organizes electron flow between a mid-potential pool (often NADH) and low-potential ferredoxin and/or protein disulfides
GO:0019420 dissimilatory sulfate reduction	IMP ferreira2023unravelingthemetabolic	NEW	Summary: The FlxABCD-HdrABC complex containing HdrA is essential for dissimilatory sulfate reduction in D. vulgaris, coupling electron transfer to the DsrC sulfur carrier. Reason: HdrA participates in dissimilatory sulfate reduction through its role in the FlxABCD-HdrABC complex. The complex interacts directly with DsrC, the key sulfur carrier in the Dsr pathway. This biological process annotation would accurately represent the physiological context of HdrA function. Supporting Evidence: ferreira2023unravelingthemetabolic FlxABCD-HdrABC ensemble as a central node connecting NADH, ferredoxin, and DsrC redox pools ferreira2023unravelingthemetabolic direct physical interaction of DsrC with the HdrABC-FlxABCD ensemble was confirmed by pull-down
GO:0005737 cytoplasm	IDA ferreira2023unravelingthemetabolic	NEW	Summary: HdrABC and FlxABCD constitute a soluble cytoplasmic complex. Reason: The FlxABCD-HdrABC complex is a soluble cytoplasmic enzyme system. HdrA lacks transmembrane domains and its redox partners (NAD(H), ferredoxin, DsrC) are cytosolic. This cellular component annotation is appropriate. Supporting Evidence: ferreira2023unravelingthemetabolic HdrABC and FlxABCD constitute a soluble cytoplasmic complex; their redox partners (NAD(H), Fdred/ox, and DsrC) are likewise cytosolic

Core Functions

HdrA is the central electron transfer hub of the FlxABCD-HdrABC complex, mediating flavin-based electron bifurcation/confurcation. It couples the oxidation of mid-potential NADH with the endergonic reduction of low-potential ferredoxin and the reduction of DsrC protein disulfide. This electron bifurcation mechanism is essential for energy conservation in D. vulgaris during both sulfate respiration and fermentative growth.

Molecular Function:

electron transfer activity

Directly Involved In:

dissimilatory sulfate reduction

Cellular Locations:

cytoplasm

HdrA contains six [4Fe-4S] clusters that form an electron transfer chain within the protein. These clusters, together with the FAD cofactor, enable the electron bifurcation mechanism by providing a pathway for electrons to flow between different redox potentials.

Molecular Function:

4 iron, 4 sulfur cluster binding

The FAD cofactor in HdrA is the site of electron bifurcation, where the flavin chemistry couples exergonic and endergonic electron transfer reactions. This is the mechanistic core of the bifurcating enzyme function.

Molecular Function:

flavin adenine dinucleotide binding

References

file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md

Deep research report on HdrA-like subunit Q72DT0 (DVU_0849)

HdrA contains six [4Fe-4S] clusters and one FAD for electron bifurcation

"HdrA contains six [4Fe–4S] clusters and one FAD"
FlxABCD-HdrABC functions as NADH dehydrogenase/heterodisulfide reductase

"composite enzyme system in D. vulgaris Hildenborough proposed to function as a novel NADH dehydrogenase/heterodisulfide reductase"
Direct interaction with DsrC confirmed by pull-down

"direct physical interaction of DsrC with the HdrABC–FlxABCD ensemble was confirmed by pull-down"
Complex is soluble and cytoplasmic

"HdrABC and FlxABCD constitute a soluble cytoplasmic complex"

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:26873250

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

High-throughput AP-MS study identifying 459 high-confidence PPIs in D. vulgaris

"We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli"
Identified Q72DT0 interactions with Q72DT1 and Q72DS8

"our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions"

PMID:27099342

Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions.

Independent validation of D. vulgaris PPIs using tagless copurification

"We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome"
Confirmed interactions between HdrABC complex subunits

"These PPIs are as strongly validated by other data as our AP-MS interactomes"

PMID:15077118

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.

Complete genome sequence establishing gene organization

"The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes"
DVU_0849 annotated as heterodisulfide reductase iron-sulfur binding subunit

"Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria"

ferreira2023unravelingthemetabolic

Unraveling the metabolic pathway of dissimilatory sulfate reduction

HdrA contains six [4Fe-4S] clusters and one FAD
FlxABCD-HdrABC functions as NADH dehydrogenase/heterodisulfide reductase
Direct physical interaction of DsrC with FlxABCD-HdrABC confirmed by pull-down
Complex is soluble and cytoplasmic
Essential for dissimilatory sulfate reduction and fermentative growth

Suggested Experiments

Experiment: Reconstitution of purified FlxABCD-HdrABC complex with defined substrates to measure electron bifurcation activity

Hypothesis: The purified complex will show NADH-dependent reduction of both ferredoxin and DsrC

Experiment: Structural determination of the FlxABCD-HdrABC complex to understand electron transfer pathways

Hypothesis: Cryo-EM or X-ray structure will reveal spatial arrangement of FAD and [4Fe-4S] clusters

Experiment: Site-directed mutagenesis of [4Fe-4S] cluster ligands to determine functional roles of individual clusters

Hypothesis: Mutation of specific cluster ligands will differentially affect electron transfer rates

📚 Additional Documentation

Deep Research Falcon

(Q72DT0-deep-research-falcon.md)

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organism: DESVH
gene_id: Q72DT0
gene_symbol: Q72DT0
uniprot_accession: Q72DT0
protein_description: 'SubName: Full=Heterodisulfide reductase, iron-sulfur-binding
subunit, putative {ECO:0000313|EMBL:AAS95329.1};'
gene_info: OrderedLocusNames=DVU_0849 {ECO:0000313|EMBL:AAS95329.1};
organism_full: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG
34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
protein_family: Belongs to the HdrA family.
protein_domains: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); FAD/NAD-bd_sf.
(IPR036188); FAD/NAD-binding_dom. (IPR023753); HdrA-like. (IPR039650)
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citation_count: 7

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: Q72DT0
Protein Description: SubName: Full=Heterodisulfide reductase, iron-sulfur-binding subunit, putative {ECO:0000313|EMBL:AAS95329.1};
Gene Information: OrderedLocusNames=DVU_0849 {ECO:0000313|EMBL:AAS95329.1};
Organism (full): Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
Protein Family: Belongs to the HdrA family.
Key Domains: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); FAD/NAD-bd_sf. (IPR036188); FAD/NAD-binding_dom. (IPR023753); HdrA-like. (IPR039650)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "Q72DT0" matches the protein description above
Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
Check if protein family/domains align with what you find in literature
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 'Q72DT0' 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 Q72DT0 (gene ID: Q72DT0, UniProt: Q72DT0) 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: Q72DT0
Protein Description: SubName: Full=Heterodisulfide reductase, iron-sulfur-binding subunit, putative {ECO:0000313|EMBL:AAS95329.1};
Gene Information: OrderedLocusNames=DVU_0849 {ECO:0000313|EMBL:AAS95329.1};
Organism (full): Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
Protein Family: Belongs to the HdrA family.
Key Domains: 4Fe4S_Fe-S-bd. (IPR017896); 4Fe4S_Fe_S_CS. (IPR017900); FAD/NAD-bd_sf. (IPR036188); FAD/NAD-binding_dom. (IPR023753); HdrA-like. (IPR039650)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "Q72DT0" matches the protein description above
Verify the organism is correct: Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris).
Check if protein family/domains align with what you find in literature
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 'Q72DT0' 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 Q72DT0 (gene ID: Q72DT0, UniProt: Q72DT0) 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.

Comprehensive research report: Q72DT0 (DVU_0849) – HdrA-like subunit from Desulfovibrio (Nitratidesulfovibrio) vulgaris Hildenborough

Verification of target identity and context
- Identity: Q72DT0 (ordered locus DVU_0849) is annotated as a heterodisulfide reductase, iron–sulfur-binding subunit, belonging to the HdrA family. HdrA subunits are soluble cytoplasmic proteins that contain multiple [4Fe–4S] clusters and an FAD for flavin-based electron bifurcation. The available 2023 synthesis on D. vulgaris Hildenborough describes HdrA with six [4Fe–4S] clusters and one FAD, consistent with an HdrA-family redox/bifurcation catalyst (supports alignment of UniProt domains: FAD/NAD-binding, 4Fe–4S-binding) (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137).
- Organism: The protein is from Desulfovibrio (Nitratidesulfovibrio) vulgaris Hildenborough, a model sulfate-reducing bacterium used to dissect energy metabolism and electron flow during sulfate respiration and fermentative growth (ferreira2023unravelingthemetabolic pages 8-16).
- Domain/family coherence: The described domain architecture—FAD/NAD-binding fold and multiple [4Fe–4S] clusters—matches the HdrA family and is concordant with bifurcating/redox-transfer functions ascribed to HdrA across anaerobes (ferreira2023unravelingthemetabolic pages 128-137).

Key concepts and definitions
- HdrABC complex: A soluble cytoplasmic heterodisulfide reductase-like complex composed of HdrA (FAD- and Fe–S–rich bifurcating subunit), HdrB (Fe–S subunit), and HdrC (small subunit), implicated in low-potential electron transfer in anaerobes. In D. vulgaris Hildenborough, HdrABC interacts directly with DsrC, the carrier protein central to sulfite reduction and sulfur trafficking in dissimilatory sulfate reduction (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137).
- FlxABCD–HdrABC system: A composite enzyme system in D. vulgaris Hildenborough proposed to function as a novel NADH dehydrogenase/heterodisulfide reductase that leverages flavin-based electron bifurcation/confurcation to couple mid-potential and low-potential redox couples, thus re-oxidizing NADH while reducing ferredoxin and/or protein-bound disulfide intermediates (e.g., on DsrC) (ferreira2023unravelingthemetabolic pages 124-128).
- Flavin-based electron bifurcation (FEB): A mechanism in which exergonic electron transfer from a mid-potential donor to an acceptor is coupled to an endergonic reduction of a low-potential acceptor via a flavin cofactor within a single protein complex; the reverse process (confurcation) merges electrons from multiple low-potential donors to reduce a higher-potential acceptor (ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).

Recent developments and latest research (emphasis 2023–2024)
- 2023 synthesis on D. vulgaris Hildenborough maps the roles of HdrABC and its DsrC interaction. It highlights: (i) HdrA contains six [4Fe–4S] clusters and one FAD; (ii) direct physical interaction of DsrC with the HdrABC–FlxABCD ensemble was confirmed by pull-down; (iii) genetic and biochemical efforts focused on expressing and purifying Hdr components; and (iv) functional coupling of the complex to steps in dissimilatory sulfate reduction and fermentative growth (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137).
- The same 2023 body of work underscores the genetic linkage of hdrABC with flxABCD and places the ensemble as a central node connecting NADH, ferredoxin, and DsrC redox pools, consistent with FEB/ECF (electron confurcation) mechanisms in Desulfovibrio (ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).
- Quantitative/proteomic context: Proteomic and modeling efforts in D. vulgaris have long implicated heterodisulfide reductase-like systems in ATP-generating electron flow; more recent integrative analyses continue to treat Hdr–Flx as a key branch point in balancing NADH, ferredoxin and sulfur carriers during different growth modes (ethanol/sulfate; fermentative). The 2023 synthesis specifically notes DsrC’s importance in fermentative growth and its direct interaction with the complex (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 194-199).

Primary function, reaction chemistry, and substrate specificity
- Catalytic role of HdrA (DVU_0849): HdrA is the bifurcating (or confurcating) FAD/Fe–S subunit that organizes electron flow between a mid-potential pool (often NADH) and low-potential ferredoxin and/or protein disulfides (notably the conserved disulfide on DsrC). It facilitates coupling that makes the endergonic reduction of ferredoxin feasible, or in reverse, merges reducing equivalents to re-oxidize low-potential carriers (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 124-128).
- FlxABCD–HdrABC overall chemistry: In D. vulgaris Hildenborough, the system functions as a novel NADH dehydrogenase/heterodisulfide reductase ensemble, mediating: NADH oxidation → exergonic branch to an acceptor and coupled endergonic branch to ferredoxin reduction; and/or confurcation of reduced ferredoxin and other donors to reduce NAD+ or a protein disulfide acceptor on DsrC. These reactions integrate with sulfite reduction via the Dsr pathway, in which DsrC acts as a key sulfur-carrier co-substrate (ferreira2023unravelingthemetabolic pages 124-128, ferreira2023unravelingthemetabolic pages 1-8).
- Electron donors and acceptors: Donor—NADH (via the FlxABCD module linked to HdrA’s FAD). Acceptors—low-potential ferredoxin and DsrC (through its conserved disulfide/sulfur carrier chemistry), with HdrB/C forming additional Fe–S electron transfer conduits (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 124-128).

Protein partners and pathway placement
- DsrC interaction: Pull-down experiments identify DsrC as a direct interaction partner of HdrABC/FlxABCD in D. vulgaris Hildenborough, supporting a model where Hdr-mediated electron flow is tightly coupled to the DsrAB/DsrC steps of dissimilatory sulfite reduction (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137).
- Genetic context: hdrABC genes are genetically linked with flxABCD, forming an operon-level association that co-evolves with ethanol metabolism and sulfate respiration modules; this organization supports the bifurcation/confurcation function connecting NADH, ferredoxin, and DsrC redox pools (ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).
- Subcellular localization: HdrABC and FlxABCD constitute a soluble cytoplasmic complex; their redox partners (NAD(H), Fdred/ox, and DsrC) are likewise cytosolic, consistent with intracellular FEB at the interface of central metabolism and the Dsr pathway (ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 194-199).

Current applications and implementations
- Bioenergetics and metabolic engineering: Understanding HdrA-centered FEB in D. vulgaris is critical for modeling and engineering electron flow in sulfate-reducing bacteria, especially under fermentative or ethanol/sulfate growth where balancing NADH, ferredoxin, and sulfur carriers determines yields and redox economy (supported by the 2023 synthesis that highlights the fermentative role of DsrC and its direct coupling to FlxABCD–HdrABC) (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).
- Environmental relevance: Because D. vulgaris Hildenborough is a model for sulfate-reducing communities implicated in biogeochemical sulfur cycling, corrosion, and bioremediation, mechanistic clarity of HdrA/Flx–Hdr function informs predictive models and interventions; the 2023 synthesis consolidates this placement by linking HdrA-mediated electron routing to the core Dsr pathway via DsrC (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 194-199).

Expert opinions and analysis from authoritative sources
- The 2023 integrative analyses emphasize HdrA as an Fe–S- and FAD-bearing bifurcating hub, with experimental evidence for physical coupling to DsrC in D. vulgaris Hildenborough and operonic association with flxABCD. These analyses advocate a central role for the FlxABCD–HdrABC ensemble in redox balancing during sulfate respiration and fermentations (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).

Relevant statistics and data
- Structural cofactor inventory: HdrA contains six [4Fe–4S] clusters and one FAD, and HdrB contains two [4Fe–4S] clusters in the D. vulgaris Hildenborough system, consistent with a high-capacity intracomplex electron transfer network needed for bifurcation/confurcation (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137).
- Experimental interactions: Direct interaction of DsrC with the FlxABCD–HdrABC complex in D. vulgaris Hildenborough has been demonstrated via pull-down assays, placing DsrC as a physiologically relevant acceptor/partner for the complex (ferreira2023unravelingthemetabolic pages 8-16).

Evidence limitations and notes
- While multiple lines of recent evidence (2023 synthesis) document domain architecture, complex composition, DsrC interactions, and genetic context, detailed kinetic parameters and full reconstitutions remain challenging; expression/purification of Hdr components can be difficult, and some electron transfer assays between Hdr variants and DsrC have proven inconclusive to date (ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 194-199).

Identity and evidence summary table
| Category | Detail | Evidence/Citation IDs |
|-------------------------|---------------------------------------------------------------------------------------------|-------------------------------------|
| Protein identity | UniProt Q72DT0, DVU_0849; HdrA family | (ferreira2023unravelingthemetabolic pages 1-8) |
| Organism | D. vulgaris Hildenborough | (ferreira2023unravelingthemetabolic pages 8-16) |
| Domain architecture | FAD/NAD-binding, multiple [4Fe-4S] clusters | (ferreira2023unravelingthemetabolic pages 128-137) |
| Complex/partners | FlxABCD–HdrABC; DsrC interaction; ferredoxin/NADH | (ferreira2023unravelingthemetabolic pages 194-199) |
| Reaction/mechanism | Electron bifurcation/confurcation; role in dissimilatory sulfate reduction | (ferreira2023unravelingthemetabolic pages 124-128) |
| Genetic context | hdrABC with flxABCD operon | (ferreira2023unravelingthemetabolic pages 194-199) |
| Localization | Cytoplasmic/soluble complex | (ferreira2023unravelingthemetabolic pages 128-137) |
| 2023–2024 evidence pointers | HdrA's role linked to electron transfer processes and interactions with DsrC highlighted | (ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137) |

Table: This table summarizes the identity and functional annotations of the gene Q72DT0 (DVU_0849) in Desulfovibrio vulgaris Hildenborough, providing evidence-backed insights into its role and mechanisms.

Links and dates (where available)
- The 2023 synthesis cited above consolidates recent biochemical and genetic findings on HdrA/FlxABCD–HdrABC in D. vulgaris Hildenborough, including DsrC interactions and cofactor composition; specific URLs were not recoverable from the extracted evidence segments and thus are not listed (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).

Conclusions
- Q72DT0 (DVU_0849) encodes an HdrA-family subunit in D. vulgaris Hildenborough that functions as the bifurcating/ confurcating core of the cytosolic FlxABCD–HdrABC ensemble. This system couples NADH with low-potential ferredoxin and the protein disulfide chemistry of DsrC, thereby integrating central metabolism with the Dsr sulfite-reduction pathway. Interaction evidence (DsrC pull-down), conserved cofactor architecture (FAD; multiple [4Fe–4S] clusters), and operonic linkage to flxABCD converge on an electron bifurcation/confurcation role that supports energy conservation and redox balance across respiratory and fermentative states (ferreira2023unravelingthemetabolic pages 1-8, ferreira2023unravelingthemetabolic pages 8-16, ferreira2023unravelingthemetabolic pages 128-137, ferreira2023unravelingthemetabolic pages 194-199, ferreira2023unravelingthemetabolic pages 124-128).

References

(ferreira2023unravelingthemetabolic pages 8-16): DMA Ferreira. Unraveling the metabolic pathway of dissimilatory sulfate reduction. Unknown journal, 2023.
(ferreira2023unravelingthemetabolic pages 128-137): DMA Ferreira. Unraveling the metabolic pathway of dissimilatory sulfate reduction. Unknown journal, 2023.
(ferreira2023unravelingthemetabolic pages 1-8): DMA Ferreira. Unraveling the metabolic pathway of dissimilatory sulfate reduction. Unknown journal, 2023.
(ferreira2023unravelingthemetabolic pages 124-128): DMA Ferreira. Unraveling the metabolic pathway of dissimilatory sulfate reduction. Unknown journal, 2023.
(ferreira2023unravelingthemetabolic pages 194-199): DMA Ferreira. Unraveling the metabolic pathway of dissimilatory sulfate reduction. Unknown journal, 2023.

Citations

ferreira2023unravelingthemetabolic pages 8-16
ferreira2023unravelingthemetabolic pages 128-137
ferreira2023unravelingthemetabolic pages 124-128
ferreira2023unravelingthemetabolic pages 1-8
ferreira2023unravelingthemetabolic pages 194-199
4Fe–4S
4Fe-4S

📄 View Raw YAML

id: Q72DT0
gene_symbol: DVU_0849
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:882
  label: Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris Hildenborough)
description: |
  HdrA is the FAD- and iron-sulfur cluster-containing subunit of the cytoplasmic
  FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. This protein
  functions as the bifurcating/confurcating core of the complex, containing six
  [4Fe-4S] clusters and one FAD cofactor that enable flavin-based electron
  bifurcation (FEB). The FlxABCD-HdrABC ensemble acts as a novel NADH
  dehydrogenase/heterodisulfide reductase that couples mid-potential NADH oxidation
  with endergonic low-potential ferredoxin reduction and DsrC protein disulfide
  chemistry. This electron coupling is essential for energy conservation during
  dissimilatory sulfate reduction and fermentative growth. HdrA belongs to the HdrA
  protein family and is homologous to heterodisulfide reductase subunits found in
  methanogens, though in sulfate-reducing bacteria it partners with the DsrC sulfur
  carrier rather than CoM-CoB heterodisulfide.
existing_annotations:
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: |
      HdrA functions as the FAD-containing bifurcating subunit of the FlxABCD-HdrABC
      complex, mediating electron transfer between NADH, ferredoxin, and DsrC
      (Ferreira 2023). The term "oxidoreductase activity" is accurate but very general
      for a protein with such specific electron bifurcation function.
    action: ACCEPT
    reason: |
      The IEA annotation based on InterPro domain IPR023753 (FAD/NAD-binding domain)
      correctly identifies oxidoreductase activity. While this term is broad, it
      accurately captures the fundamental catalytic function. More specific terms
      for electron bifurcation activity do not yet exist in GO. The protein's
      FAD-dependent electron transfer function in the FlxABCD-HdrABC complex is
      well-documented (Ferreira 2023).
    supported_by:
      - reference_id: file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md
        supporting_text: "HdrA contains six [4Fe–4S] clusters and one FAD"
      - reference_id: file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md
        supporting_text: "HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit that organizes electron flow between a mid-potential pool (often NADH) and low-potential ferredoxin and/or protein disulfides"
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: |
      HdrA contains multiple iron-sulfur clusters that bind iron ions as part of
      their electron transfer function. The annotation is correct but less
      informative than the more specific iron-sulfur cluster binding terms.
    action: ACCEPT
    reason: |
      This IEA annotation based on UniProtKB keyword KW-0479 (Metal-binding) is
      correct. HdrA contains six [4Fe-4S] clusters that require iron binding
      (Ferreira 2023). While more specific annotations for 4Fe-4S cluster binding
      are also present, this general term is not incorrect and can be retained
      as it is encompassed by the more specific terms.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA contains six [4Fe-4S] clusters and one FAD"
- term:
    id: GO:0051536
    label: iron-sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: |
      HdrA contains multiple [4Fe-4S] clusters essential for its electron
      bifurcation function. Iron-sulfur cluster binding is a core molecular
      function of this protein.
    action: ACCEPT
    reason: |
      The IEA annotation based on UniProtKB keyword KW-0411 (Iron-sulfur) correctly
      identifies iron-sulfur cluster binding as a core function. HdrA contains six
      [4Fe-4S] clusters that mediate electron transfer in the bifurcating complex
      (Ferreira 2023). This annotation accurately reflects the protein's cofactor
      requirements.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA contains six [4Fe-4S] clusters and one FAD"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "conserved cofactor architecture (FAD; multiple [4Fe-4S] clusters)"
- term:
    id: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: |
      HdrA specifically contains six [4Fe-4S] clusters that are essential for
      intracomplex electron transfer during electron bifurcation/confurcation.
    action: ACCEPT
    reason: |
      This IEA annotation based on UniProtKB keyword KW-0004 (4Fe-4S) is highly
      accurate. The 2023 synthesis on D. vulgaris Hildenborough documents that
      HdrA contains six [4Fe-4S] clusters (Ferreira 2023). The UniProt entry also
      contains two annotated 4Fe-4S ferredoxin-type domains (positions 542-571
      and 572-601). This is a core molecular function annotation.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA contains six [4Fe-4S] clusters and one FAD"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "Structural cofactor inventory: HdrA contains six [4Fe-4S] clusters and one FAD"
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26873250
  supporting_entities:
    - UniProtKB:Q72DS8
  review:
    summary: |
      High-throughput AP-MS study in D. vulgaris identified interaction between
      Q72DT0 (HdrA/DVU_0849) and Q72DS8 (DVU_0851). Q72DS8 is likely HdrC or a
      Flx subunit based on genomic context. This interaction is biologically
      meaningful as HdrA functions within the FlxABCD-HdrABC complex.
    action: MODIFY
    reason: |
      While the protein-protein interaction is experimentally validated (IPI evidence
      from AP-MS), the term "protein binding" (GO:0005515) is uninformative. HdrA
      physically interacts with other subunits of the FlxABCD-HdrABC complex as
      part of its electron bifurcation function. A more specific term would better
      capture the functional nature of this interaction. However, no more specific
      GO term adequately captures the interaction between electron bifurcating
      complex subunits. The interaction supports the complex formation but
      "protein binding" alone provides minimal functional insight.
    proposed_replacement_terms:
      - id: GO:0009055
        label: electron transfer activity
    supported_by:
      - reference_id: PMID:26873250
        supporting_text: "459 high confidence PPIs from D. vulgaris"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "FlxABCD-HdrABC system: A composite enzyme system in D. vulgaris Hildenborough proposed to function as a novel NADH dehydrogenase/heterodisulfide reductase"
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26873250
  supporting_entities:
    - UniProtKB:Q72DT1
  review:
    summary: |
      AP-MS study identified interaction between Q72DT0 (HdrA/DVU_0849) and Q72DT1
      (DVU_0848). Q72DT1 is the adjacent gene product, likely HdrB based on operon
      organization. UniProt records 3 experiments supporting this interaction.
    action: MODIFY
    reason: |
      The interaction with Q72DT1 (DVU_0848) is experimentally validated and
      biologically meaningful - this represents HdrA-HdrB interaction within
      the heterodisulfide reductase complex. However, "protein binding" is too
      generic. The HdrA-HdrB interaction is essential for the electron bifurcation
      mechanism, where HdrB contains additional [4Fe-4S] clusters that receive
      electrons from HdrA.
    proposed_replacement_terms:
      - id: GO:0009055
        label: electron transfer activity
    supported_by:
      - reference_id: PMID:26873250
        supporting_text: "459 high confidence PPIs from D. vulgaris"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrB contains two [4Fe-4S] clusters in the D. vulgaris Hildenborough system"
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27099342
  supporting_entities:
    - UniProtKB:Q72DS8
  review:
    summary: |
      Independent validation of Q72DT0-Q72DS8 interaction via quantitative tagless
      copurification method. This study confirmed PPIs from the AP-MS interactome
      with high confidence.
    action: MODIFY
    reason: |
      This represents independent experimental validation of the HdrA interaction
      with another complex subunit (Q72DS8/DVU_0851). The tagless copurification
      method provides orthogonal support for the AP-MS data. However, the annotation
      as "protein binding" remains uninformative for understanding the functional
      role of this interaction within the electron bifurcating complex.
    proposed_replacement_terms:
      - id: GO:0009055
        label: electron transfer activity
    supported_by:
      - reference_id: PMID:27099342
        supporting_text: "200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome"
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27099342
  supporting_entities:
    - UniProtKB:Q72DT1
  review:
    summary: |
      Independent validation of Q72DT0-Q72DT1 (HdrA-HdrB) interaction via
      quantitative tagless copurification. UniProt records 5 experiments total
      supporting this interaction.
    action: MODIFY
    reason: |
      Strong experimental support from multiple independent methods confirms
      the HdrA-HdrB interaction. This is a core functional interaction within
      the FlxABCD-HdrABC complex. The generic "protein binding" term should be
      supplemented or replaced with more informative functional terms.
    proposed_replacement_terms:
      - id: GO:0009055
        label: electron transfer activity
    supported_by:
      - reference_id: PMID:27099342
        supporting_text: "200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrABC interacts directly with DsrC"
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: |
      HdrA contains one FAD cofactor that is essential for its electron
      bifurcation function. FAD binding is a core molecular function.
    action: NEW
    reason: |
      UniProt annotates FAD as a cofactor for this protein (ECO:0000256|ARBA:ARBA00001974).
      The deep research confirms HdrA contains FAD which is central to flavin-based
      electron bifurcation mechanism. This annotation should be present but appears
      missing from the GOA file despite being in UniProt.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA contains six [4Fe-4S] clusters and one FAD"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit"
- term:
    id: GO:0009055
    label: electron transfer activity
  evidence_type: ISS
  original_reference_id: ferreira2023unravelingthemetabolic
  review:
    summary: |
      HdrA functions as an electron transfer hub in the FlxABCD-HdrABC complex,
      mediating electron flow between NADH, ferredoxin, and DsrC.
    action: NEW
    reason: |
      This is a core function of HdrA that is well-documented but not explicitly
      annotated. HdrA mediates electron transfer via its FAD and [4Fe-4S] clusters
      as part of flavin-based electron bifurcation. This annotation would more
      accurately capture the protein's primary molecular function than the current
      generic annotations.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrA is the bifurcating (or confurcating) FAD/Fe-S subunit that organizes electron flow between a mid-potential pool (often NADH) and low-potential ferredoxin and/or protein disulfides"
- term:
    id: GO:0019420
    label: dissimilatory sulfate reduction
  evidence_type: IMP
  original_reference_id: ferreira2023unravelingthemetabolic
  review:
    summary: |
      The FlxABCD-HdrABC complex containing HdrA is essential for dissimilatory
      sulfate reduction in D. vulgaris, coupling electron transfer to the DsrC
      sulfur carrier.
    action: NEW
    reason: |
      HdrA participates in dissimilatory sulfate reduction through its role in
      the FlxABCD-HdrABC complex. The complex interacts directly with DsrC, the
      key sulfur carrier in the Dsr pathway. This biological process annotation
      would accurately represent the physiological context of HdrA function.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "FlxABCD-HdrABC ensemble as a central node connecting NADH, ferredoxin, and DsrC redox pools"
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "direct physical interaction of DsrC with the HdrABC-FlxABCD ensemble was confirmed by pull-down"
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: ferreira2023unravelingthemetabolic
  review:
    summary: |
      HdrABC and FlxABCD constitute a soluble cytoplasmic complex.
    action: NEW
    reason: |
      The FlxABCD-HdrABC complex is a soluble cytoplasmic enzyme system. HdrA
      lacks transmembrane domains and its redox partners (NAD(H), ferredoxin,
      DsrC) are cytosolic. This cellular component annotation is appropriate.
    supported_by:
      - reference_id: ferreira2023unravelingthemetabolic
        supporting_text: "HdrABC and FlxABCD constitute a soluble cytoplasmic complex; their redox partners (NAD(H), Fdred/ox, and DsrC) are likewise cytosolic"
references:
- id: file:DESVH/Q72DT0/Q72DT0-deep-research-falcon.md
  title: Deep research report on HdrA-like subunit Q72DT0 (DVU_0849)
  findings:
    - statement: HdrA contains six [4Fe-4S] clusters and one FAD for electron bifurcation
      supporting_text: "HdrA contains six [4Fe–4S] clusters and one FAD"
    - statement: FlxABCD-HdrABC functions as NADH dehydrogenase/heterodisulfide reductase
      supporting_text: "composite enzyme system in D. vulgaris Hildenborough proposed to function as a novel NADH dehydrogenase/heterodisulfide reductase"
    - statement: Direct interaction with DsrC confirmed by pull-down
      supporting_text: "direct physical interaction of DsrC with the HdrABC–FlxABCD ensemble was confirmed by pull-down"
    - statement: Complex is soluble and cytoplasmic
      supporting_text: "HdrABC and FlxABCD constitute a soluble cytoplasmic complex"
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  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:
    - statement: High-throughput AP-MS study identifying 459 high-confidence PPIs in D. vulgaris
      supporting_text: "We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli"
    - statement: Identified Q72DT0 interactions with Q72DT1 and Q72DS8
      supporting_text: "our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions"
- id: PMID:27099342
  title: 'Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein
    Interactions.'
  findings:
    - statement: Independent validation of D. vulgaris PPIs using tagless copurification
      supporting_text: "We also identify 200 high confidence D. vulgaris PPIs based on tagless copurification and colocalization in the genome"
    - statement: Confirmed interactions between HdrABC complex subunits
      supporting_text: "These PPIs are as strongly validated by other data as our AP-MS interactomes"
- id: PMID:15077118
  title: 'The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio
    vulgaris Hildenborough.'
  findings:
    - statement: Complete genome sequence establishing gene organization
      supporting_text: "The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes"
    - statement: DVU_0849 annotated as heterodisulfide reductase iron-sulfur binding subunit
      supporting_text: "Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria"
- id: ferreira2023unravelingthemetabolic
  title: 'Unraveling the metabolic pathway of dissimilatory sulfate reduction'
  findings:
    - statement: HdrA contains six [4Fe-4S] clusters and one FAD
    - statement: FlxABCD-HdrABC functions as NADH dehydrogenase/heterodisulfide reductase
    - statement: Direct physical interaction of DsrC with FlxABCD-HdrABC confirmed by pull-down
    - statement: Complex is soluble and cytoplasmic
    - statement: Essential for dissimilatory sulfate reduction and fermentative growth
core_functions:
- molecular_function:
    id: GO:0009055
    label: electron transfer activity
  description: |
    HdrA is the central electron transfer hub of the FlxABCD-HdrABC complex,
    mediating flavin-based electron bifurcation/confurcation. It couples the
    oxidation of mid-potential NADH with the endergonic reduction of low-potential
    ferredoxin and the reduction of DsrC protein disulfide. This electron
    bifurcation mechanism is essential for energy conservation in D. vulgaris
    during both sulfate respiration and fermentative growth.
  directly_involved_in:
    - id: GO:0019420
      label: dissimilatory sulfate reduction
  locations:
    - id: GO:0005737
      label: cytoplasm
- molecular_function:
    id: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
  description: |
    HdrA contains six [4Fe-4S] clusters that form an electron transfer chain
    within the protein. These clusters, together with the FAD cofactor, enable
    the electron bifurcation mechanism by providing a pathway for electrons
    to flow between different redox potentials.
- molecular_function:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  description: |
    The FAD cofactor in HdrA is the site of electron bifurcation, where the
    flavin chemistry couples exergonic and endergonic electron transfer
    reactions. This is the mechanistic core of the bifurcating enzyme function.
proposed_new_terms: []
suggested_questions:
- question: What is the precise stoichiometry of the FlxABCD-HdrABC complex?
- question: Does HdrA directly interact with DsrC, or is this interaction mediated through other subunits?
- question: What are the redox potentials of the individual [4Fe-4S] clusters in HdrA?
suggested_experiments:
- description: Reconstitution of purified FlxABCD-HdrABC complex with defined substrates to measure electron bifurcation activity
  hypothesis: The purified complex will show NADH-dependent reduction of both ferredoxin and DsrC
- description: Structural determination of the FlxABCD-HdrABC complex to understand electron transfer pathways
  hypothesis: Cryo-EM or X-ray structure will reveal spatial arrangement of FAD and [4Fe-4S] clusters
- description: Site-directed mutagenesis of [4Fe-4S] cluster ligands to determine functional roles of individual clusters
  hypothesis: Mutation of specific cluster ligands will differentially affect electron transfer rates

DVU_0849

Gene Description

Existing Annotations Review

Core Functions

HdrA contains six [4Fe-4S] clusters that form an electron transfer chain within the protein. These clusters, together with the FAD cofactor, enable the electron bifurcation mechanism by providing a pathway for electrons to flow between different redox potentials.

The FAD cofactor in HdrA is the site of electron bifurcation, where the flavin chemistry couples exergonic and endergonic electron transfer reactions. This is the mechanistic core of the bifurcating enzyme function.

References

Suggested Questions for Experts

Suggested Experiments

📚 Additional Documentation

Deep Research Falcon

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

Research Target:

Output

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

Target Gene/Protein Identity (from UniProt):

MANDATORY VERIFICATION STEPS:

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

Research Target:

Citations

📄 View Raw YAML