sdhA

UniProt ID: Q88FA7
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

Flavoprotein (catalytic) subunit of succinate dehydrogenase (respiratory Complex II) in Pseudomonas putida KT2440. SdhA carries a covalently bound FAD cofactor and the succinate/fumarate active site, catalysing the oxidation of succinate to fumarate with transfer of electrons into the membrane quinone pool (EC 1.3.5.1). This reaction couples the tricarboxylic acid (TCA) cycle to the aerobic respiratory electron transport chain. SdhA forms the soluble catalytic head of the four-subunit enzyme together with the iron-sulfur subunit SdhB (PP_4190) and the membrane anchor subunits SdhD (PP_4192) and SdhC (PP_4193), to which it is peripherally attached on the cytoplasmic face of the inner (plasma) membrane. FAD incorporation (flavinylation) depends on the accessory assembly factor SdhE.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0000104 succinate dehydrogenase activity
IEA
GO_REF:0000118 		ACCEPT
Summary: SdhA is the flavoprotein catalytic subunit of succinate dehydrogenase (Complex II); succinate dehydrogenase activity is its core molecular function.
Reason: Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.
GO:0005886 plasma membrane
IEA
GO_REF:0000120 		ACCEPT
Summary: SdhA is a peripheral membrane protein attached to the cytoplasmic (inner) face of the inner/plasma membrane as part of the membrane-bound Complex II.
Reason: Matches UniProt subcellular location (Cell inner membrane; peripheral membrane protein; cytoplasmic side). In Gram-negative bacteria the inner membrane is the GO plasma membrane.
GO:0006099 tricarboxylic acid cycle
IEA
GO_REF:0000120 		ACCEPT
Summary: Succinate dehydrogenase catalyses the succinate-to-fumarate step of the TCA cycle; this is a core biological process for SdhA.
Reason: Supported by UniProt pathway annotation (tricarboxylic acid cycle; fumarate from succinate, step 1/1) and conserved enzyme function.
GO:0008177 succinate dehydrogenase (quinone) activity
IEA
GO_REF:0000120 		ACCEPT
Summary: This is the precise quinone-coupled reaction (succinate + quinone = fumarate + quinol, RHEA:40523, EC 1.3.5.1) catalysed by the holo-enzyme to which SdhA contributes the catalytic flavoprotein head.
Reason: Directly matches the UniProt CATALYTIC ACTIVITY (RHEA:40523) and EC 1.3.5.1. Most informative molecular-function term for the complex's overall reaction.
GO:0009055 electron transfer activity
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: SdhA participates in electron transfer, passing electrons abstracted from succinate via FAD toward the iron-sulfur clusters of SdhB and the quinone pool.
Reason: Biologically true but more generic than the specific succinate dehydrogenase (quinone) activity that captures SdhA's core function. Retain as supporting/non-core rather than primary.
GO:0009061 anaerobic respiration
IEA
GO_REF:0000118 		MARK AS OVER ANNOTATED
Summary: This subunit is the forward/aerobic succinate dehydrogenase flavoprotein (TIGR01816 sdhA_forward), not the fumarate reductase used in anaerobic respiration.
Reason: UniProt notes that two distinct FAD enzymes interconvert fumarate and succinate, with fumarate reductase (FrdA) used in anaerobic growth and succinate dehydrogenase used in aerobic growth. The forward SdhA is assigned to aerobic respiration; this TreeGrafter-propagated anaerobic respiration term reflects the broader SdhA/FrdA family and over-annotates the aerobic SdhA.
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002 		KEEP AS NON CORE
Summary: Generic parent of the specific succinate dehydrogenase (quinone) activity already annotated.
Reason: Correct but uninformative high-level term; subsumed by the specific EC 1.3.5.1 annotation. Retain as non-core.
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
IEA
GO_REF:0000120 		KEEP AS NON CORE
Summary: Accurate intermediate-level description of the chemistry (oxidation of the succinate CH-CH bond to the fumarate C=C bond), but less specific than succinate dehydrogenase (quinone) activity.
Reason: Correct grouping term but subsumed by the specific MF term; keep as non-core supporting annotation.
GO:0022900 electron transport chain
IEA
GO_REF:0000120 		ACCEPT
Summary: Complex II feeds electrons from succinate into the respiratory quinone pool, contributing to the aerobic electron transport chain.
Reason: Supported by UniProt (electron transport keyword) and the established role of Complex II linking the TCA cycle to respiration.
GO:0050660 flavin adenine dinucleotide binding
IEA
GO_REF:0000120 		ACCEPT
Summary: SdhA binds a (covalently attached) FAD cofactor essential for succinate oxidation.
Reason: Supported by UniProt COFACTOR (FAD), multiple conserved FAD-binding residues, the Tele-8alpha-FAD histidine modified residue, and SdhE-dependent flavinylation.
GO:0160308 succinate dehydrogenase (FAD) activity
IEA
GO_REF:0000002 		ACCEPT
Summary: Describes the FAD-dependent succinate->fumarate half-reaction occurring at the SdhA flavin site, prior to electron transfer to quinone.
Reason: Accurately captures the FAD-coupled catalytic step intrinsic to the SdhA subunit; complementary to the holo-enzyme quinone-coupled term GO:0008177. Both are valid and informative.

Core Functions

Catalytic flavoprotein subunit of succinate dehydrogenase (Complex II) that oxidises succinate to fumarate using a covalently bound FAD cofactor, the rate-limiting catalytic step linking the TCA cycle to the respiratory chain.

Molecular Function:
succinate dehydrogenase (quinone) activity
Directly Involved In:
tricarboxylic acid cycle
Supporting Evidence:
  • GO_REF:0000120
    UniProt CATALYTIC ACTIVITY a quinone + succinate = fumarate + a quinol (RHEA:40523, EC 1.3.5.1).

Binds FAD at the catalytic head to abstract electrons from succinate and feed them into the electron transport chain via the SdhB iron-sulfur clusters and the membrane quinone pool.

Molecular Function:
flavin adenine dinucleotide binding
Directly Involved In:
electron transport chain
Supporting Evidence:
  • GO_REF:0000120
    UniProt COFACTOR FAD; conserved FAD-binding residues and Tele-8alpha-FAD histidine.

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000118
TreeGrafter-generated GO annotations
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
PMID:22474332
SdhE is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria
  • The accessory protein SdhE binds FAD and is required for flavinylation of the succinate dehydrogenase flavoprotein subunit (SdhA) and for SDH activity in bacteria.

Suggested Questions for Experts

Q: Has the SdhA-SdhBCD Complex II of P. putida KT2440 been biochemically characterised (kinetics, FAD content, quinone specificity), and does it show any fumarate reductase activity in vitro?

Suggested Experiments

Experiment: Purify the P. putida KT2440 SdhABCD complex and measure succinate:quinone oxidoreductase kinetics and FAD flavinylation status, with and without SdhE, to confirm the conserved mechanism in this organism.

Deep Research

Falcon

(sdhA-deep-research-falcon.md)
Research Report: Functional Annotation of **sdhA** (PP_4191; UniProt Q88FA7) in *Pseudomonas putida* KT2440 Falcon Edison Scientific Literature 14 citations 2 artifacts 2026-06-11T22:36:14.747032
Edison artifact artifact-00 (text/markdown)
## Context ID: pqac-00000005 Table 1 (found on page 3) provides physiological characteristics of P. putida MAD2 and its mutants. While it does not list the spec (image/png)

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: Functional Annotation of sdhA (PP_4191; UniProt Q88FA7) in Pseudomonas putida KT2440

0. Target verification (mandatory disambiguation)

The gene symbol sdhA in Pseudomonas putida KT2440 is unambiguously linked to PP_4191, annotated as the succinate dehydrogenase flavoprotein subunit (SdhA), and occurs with the other complex II subunits SdhB (PP_4190), SdhD (PP_4192), and SdhC (PP_4193) in KT2440. This mapping matches the UniProt-provided identity (Q88FA7) as a succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1). (chavarria2012regulatorytasksof pages 3-4, chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)

1. Key concepts, definitions, and current understanding

1.1 What SdhA is (protein role within Complex II)

Succinate dehydrogenase (SDH; respiratory complex II) is a central bioenergetic enzyme that functionally couples the tricarboxylic acid (TCA) cycle to the aerobic respiratory electron transport chain. In bacteria and mitochondria, complex II comprises a soluble catalytic “head” and membrane anchor components that connect catalysis to the quinone pool. (bouillaud2023inhibitionofsuccinate pages 3-5, mcneil2012sdheisa pages 1-2)

Within this complex, SdhA is the flavoprotein catalytic subunit that carries the flavin cofactor and hosts the succinate/fumarate active-site chemistry. (bouillaud2023inhibitionofsuccinate pages 3-5, mcneil2012sdheisa pages 1-2)

1.2 Enzymatic reaction and substrate specificity (primary function)

The canonical SDH reaction (EC 1.3.5.1) is the oxidation of succinate to fumarate:

  • succinate → fumarate + 2H+ + 2e−

The electrons are transferred into the membrane quinone pool by coupled reduction of quinone:

  • Q + 2e− + 2H+ → QH2

Thus, SdhA’s primary substrate specificity is toward succinate (as the electron donor in the forward SDH direction) and fumarate (in the reverse fumarate reductase direction in organisms/conditions where reversal occurs), with coupling to the quinone pool as electron acceptor via the rest of complex II. (bouillaud2023inhibitionofsuccinate pages 3-5)

1.3 Cofactors/prosthetic groups and maturation concepts

Complex II function depends on redox cofactors:

  • SDH contains FAD (associated with the soluble catalytic portion containing SdhA) and iron (consistent with iron-containing redox centers in the soluble part of the complex). (bouillaud2023inhibitionofsuccinate pages 3-5)

A key mechanistic concept for bacterial SdhA is flavinylation (incorporation/attachment of FAD into the SdhA subunit). In a bacterial model system, SdhA requires an accessory protein SdhE for FAD incorporation; SdhE interacts with SdhA, binds FAD, and is required for SdhA flavinylation and SDH activity. (mcneil2012sdheisa pages 4-5, mcneil2012sdheisa pages 1-2)

Although this SdhE-dependent maturation evidence is not from P. putida directly, SdhE is described as conserved across diverse proteobacteria, supporting inference that P. putida SdhA likewise depends on proper flavinylation for activity. (mcneil2012sdheisa pages 1-2)

2. Pathway context and cellular localization in Pseudomonas putida KT2440

2.1 Localization

Complex II is described as a membrane-spanning redox enzyme with a soluble catalytic side containing the flavoprotein subunit (SdhA) and membrane subunits that inject electrons into quinone in the membrane. (bouillaud2023inhibitionofsuccinate pages 3-5)

Consistent with this, bacterial experimental work localized SdhA to the membrane-associated complex, reflecting its function as part of a membrane respiratory complex rather than a freely soluble cytosolic enzyme. (mcneil2012sdheisa pages 4-5)

2.2 Subunits/operon context in KT2440

In KT2440, the complex II subunits are explicitly mapped as:

  • SdhB (iron–sulfur subunit): PP_4190
  • SdhA (flavoprotein subunit): PP_4191
  • SdhD (hydrophobic membrane anchor): PP_4192
  • SdhC (cytochrome b556 subunit): PP_4193

This supports annotation of PP_4191/Q88FA7 as the catalytic complex II flavoprotein subunit within the canonical SDH architecture in P. putida KT2440. (chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)

3. Recent developments (prioritizing 2023–2024) and latest research relevant to sdhA/complex II

3.1 2023: SDH function contextualized by modern bioenergetics and inhibition literature

A 2023 review synthesizes modern understanding of SDH/complex II as a redox enzyme connecting succinate oxidation to quinone reduction, emphasizing its four-subunit architecture and centrality to energy metabolism, while also discussing assay approaches and the energetic consequence that complex II does not pump protons (unlike complexes I/III/IV), implying its control is primarily redox/substrate/quinone-state dependent. (bouillaud2023inhibitionofsuccinate pages 3-5)

While this review focuses on SDH inhibition in eukaryotic contexts, its biochemical statements about the enzyme’s reaction chemistry and architecture are directly applicable to bacterial SDH (including P. putida). (bouillaud2023inhibitionofsuccinate pages 3-5)

3.2 2023: KT2440 microaerobic regulation of sdhA and metabolic engineering implications

A 2023 study on microaerobic cultivation of P. putida KT2440 for succinate production provides direct KT2440 evidence that:

  • KT2440 can reassimilate succinate via an SDH activity (“sdhAB enzyme”), which can reduce apparent succinate accumulation in bioprocess contexts; therefore, deleting or downregulating sdhAB is proposed as a strategy to improve succinate production. (mutyala2023citratesynthaseoverexpression pages 10-11)
  • sdhA expression is reduced by ~2.2-fold under microaerobic relative to aerobic cultivation in WT KT2440, consistent with reduced succinate oxidation capacity when oxygen availability is limited. (mutyala2023citratesynthaseoverexpression pages 10-11)

Together, these findings operationalize sdhA (and sdhAB) as a tunable node in P. putida metabolic engineering for improved organic acid accumulation under oxygen-limited regimes. (mutyala2023citratesynthaseoverexpression pages 10-11)

3.3 2024 evidence limitation (explicitly stated)

Although 2024 P. putida KT2440 systems-biology papers were retrieved in the search set, the accessible text evidence obtained in this run did not provide explicit, citable sdhA-specific quantitative statements. Therefore, sdhA-focused 2023 KT2440 evidence (above) is the primary recent source for strain-specific regulation and application claims within the current tool-retrieved corpus. (mutyala2023citratesynthaseoverexpression pages 10-11)

4. Applications and real-world implementations

4.1 Industrial and metabolic engineering context (succinate bioproduction)

In KT2440 succinate bioproduction under microaerobic conditions, sdhA/SDH is relevant because it can consume succinate (reassimilate it into the TCA cycle via succinate oxidation). The 2023 microaerobic cultivation study explicitly frames sdhAB as a target whose downregulation or deletion could improve succinate accumulation and yields in engineered strains. (mutyala2023citratesynthaseoverexpression pages 10-11)

This is a practical, real-world application: controlling SDH activity (via sdhA expression or function) helps redirect carbon and reducing equivalents away from respiration-driven succinate consumption toward product accumulation. (mutyala2023citratesynthaseoverexpression pages 10-11)

5. Expert opinion and analysis (authoritative synthesis)

5.1 Why sdhA is a high-confidence functional annotation target

Multiple independent lines of evidence converge on the functional assignment:

  1. Direct KT2440 locus mapping (PP_4191 = SdhA) and subunit context (PP_4190/4192/4193), establishing correct gene identity in the correct organism/strain. (chavarria2012regulatorytasksof pages 3-4, chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)
  2. Biochemical consensus that SdhA-containing complex II catalyzes succinate oxidation coupled to quinone reduction (EC 1.3.5.1) and contains FAD and iron-based redox centers. (bouillaud2023inhibitionofsuccinate pages 3-5)
  3. Mechanistic bacterial evidence that SdhA is FAD-dependent and requires maturation (flavinylation) mediated by the conserved protein SdhE; disruption of this process dramatically reduces SDH activity. (mcneil2012sdheisa pages 4-5, mcneil2012sdheisa pages 1-2)

Thus, even if KT2440-specific enzymology (e.g., purified enzyme kinetics) is limited in the retrieved corpus, functional inference for Q88FA7 is robust because complex II is highly conserved and anchored by direct strain-specific gene mapping. (bouillaud2023inhibitionofsuccinate pages 3-5, chavarria2012regulatorytasksof pages 3-4, chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)

5.2 Regulatory interpretation under oxygen limitation

The KT2440 observation that sdhA transcript abundance drops ~2.2-fold under microaerobic cultivation can be interpreted as part of a broader physiological shift: when oxygen is limiting, cells may downshift electron transport chain activity and reduce flux through succinate oxidation, a step that normally passes electrons to quinone in aerobic respiration. (bouillaud2023inhibitionofsuccinate pages 3-5, mutyala2023citratesynthaseoverexpression pages 10-11)

6. Relevant statistics and quantitative data (from recent studies)

6.1 KT2440 sdhA expression under microaerobic vs aerobic conditions

  • ~2.2-fold reduction in sdhA expression in WT P. putida under microaerobic versus aerobic cultivation. (mutyala2023citratesynthaseoverexpression pages 10-11)

6.2 KT2440 succinate production metrics (engineering context tied to SDH control)

In the same 2023 study (microaerobic succinate production from acetate with citrate synthase overexpression):

  • gltA overexpression yielded an ~50% improvement in succinate production compared with WT. (mutyala2023citratesynthaseoverexpression pages 10-11)
  • Under optimal pH 7.5, succinate accumulation reached 4.73 ± 0.6 mM in 36 h, reported as ~400% higher than WT. (mutyala2023citratesynthaseoverexpression pages 10-11)

These values provide practical quantitative context for why minimizing SDH-mediated succinate reassimilation (e.g., via sdhAB modulation) is an attractive engineering strategy. (mutyala2023citratesynthaseoverexpression pages 10-11)

6.3 Mechanistic activity effect size for SdhA maturation disruption (bacterial model)

In a bacterial model system used to elucidate complex II flavinylation:

  • Loss of the flavin assembly factor SdhE caused a ~90% reduction in measured SDH activity, consistent with the requirement of SdhA flavinylation (FAD incorporation) for function. (mcneil2012sdheisa pages 4-5)

Evidence summary table

Topic Key findings (concise) Evidence type (review/primary; organism) Quantitative data (if any) Primary source (authors, year) Publication date (month/year if available) URL PaperQA citation id (pqac-...)
identity PP_4191 is explicitly annotated as SdhA, succinate dehydrogenase flavoprotein subunit in Pseudomonas putida KT2440, matching UniProt Q88FA7. Primary; P. putida KT2440 Not reported Chavarría et al., 2012 05/2012 https://doi.org/10.1128/mbio.00028-12 (chavarria2012regulatorytasksof pages 3-4)
reaction/EC Succinate dehydrogenase (complex II) catalyzes succinate → fumarate + 2H+ + 2e− and couples this to quinone reduction (Q → QH2), consistent with EC 1.3.5.1. Review; general SDH biology Stoichiometry given in review; no strain-specific kinetic values Bouillaud, 2023 02/2023 https://doi.org/10.3390/ijms24044045 (bouillaud2023inhibitionofsuccinate pages 3-5)
role/pathway SDH/complex II links the TCA cycle and electron transport chain; SdhA is the catalytic flavoprotein subunit of this respiratory enzyme. Review + primary; general bacteria Not reported for KT2440 Bouillaud, 2023; McNeil et al., 2012 02/2023; 05/2012 https://doi.org/10.3390/ijms24044045 ; https://doi.org/10.1074/jbc.m111.293803 (bouillaud2023inhibitionofsuccinate pages 3-5, mcneil2012sdheisa pages 1-2)
cofactors Bacterial SdhA is a FAD-dependent flavoprotein; SDH contains FAD and iron cofactors, and SdhE is required for SdhA flavinylation in bacteria. Review + primary; general bacteria Loss of SdhE caused ~90% reduction in SDH activity in Serratia model McNeil et al., 2012; Bouillaud, 2023 05/2012; 02/2023 https://doi.org/10.1074/jbc.m111.293803 ; https://doi.org/10.3390/ijms24044045 (mcneil2012sdheisa pages 4-5, bouillaud2023inhibitionofsuccinate pages 3-5, mcneil2012sdheisa pages 1-2)
complex subunits/operon In KT2440, the SDH subunits are mapped as SdhB/PP_4190, SdhA/PP_4191, SdhD/PP_4192, and SdhC/PP_4193. This supports assignment of PP_4191 to the canonical bacterial SDH complex. Primary; P. putida KT2440 Not reported Chavarría et al., 2012 05/2012 https://doi.org/10.1128/mbio.00028-12 (chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)
localization SDH is a membrane-spanning complex with a soluble catalytic side containing SdhA and membrane subunits that transfer electrons to quinone; bacterial experiments localized SdhA to the membrane-associated complex. Review + primary; general bacteria Functional SDH reported as ~360 kDa trimeric complex in Serratia model Bouillaud, 2023; McNeil et al., 2012 02/2023; 05/2012 https://doi.org/10.3390/ijms24044045 ; https://doi.org/10.1074/jbc.m111.293803 (mcneil2012sdheisa pages 4-5, bouillaud2023inhibitionofsuccinate pages 3-5)
regulation/expression In P. putida, sdhA expression decreases under microaerobic cultivation, consistent with reduced succinate oxidation when oxygen becomes limiting. Primary; P. putida ~2.2-fold reduction of sdhA expression in wild type under microaerobic vs aerobic conditions Mutyala et al., 2023 07/2023 https://doi.org/10.1021/acsomega.3c02520 (mutyala2023citratesynthaseoverexpression pages 10-11)
phenotypes/essentiality KT2440 transposon screening identified the succinate dehydrogenase complex (5 genes) among genes important for growth on minimal medium, supporting central metabolic importance, though not proving PP_4191 alone is universally essential. Primary; P. putida KT2440 Gene count only; no PP_4191-specific effect size in provided context Molina-Henares et al., 2010 06/2010 https://doi.org/10.1111/j.1462-2920.2010.02166.x (chavarria2012regulatorytasksof pages 3-4)
applications/engineering relevance Because KT2440 can reassimilate succinate using sdhAB, downregulating or deleting sdhAB is proposed to improve biotechnological succinate accumulation; microaerobic repression of sdhA supports this strategy. Primary; P. putida gltA overexpression improved succinate production by ~50%; succinate reached 4.73 ± 0.6 mM in 36 h, ~400% above wild type at pH 7.5; sdhA expression reduced ~2.2-fold microaerobically Mutyala et al., 2023 07/2023 https://doi.org/10.1021/acsomega.3c02520 (mutyala2023citratesynthaseoverexpression pages 10-11)

Table: This table summarizes evidence-supported functional annotation points for Pseudomonas putida KT2440 sdhA (PP_4191; UniProt Q88FA7), including identity, biochemistry, pathway role, localization, and engineering relevance. It only includes claims directly supported by the available evidence contexts.

References (with dates and URLs)

  • Chavarría M. et al. mBio (May 2012). “Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism.” https://doi.org/10.1128/mbio.00028-12 (chavarria2012regulatorytasksof pages 3-4, chavarria2012regulatorytasksof media b14b64f4, chavarria2012regulatorytasksof media 8dabbe7d)
  • Bouillaud F. Int J Mol Sci (Feb 2023). “Inhibition of Succinate Dehydrogenase by Pesticides (SDHIs) and Energy Metabolism.” https://doi.org/10.3390/ijms24044045 (bouillaud2023inhibitionofsuccinate pages 3-5)
  • McNeil M.B. et al. J Biol Chem (May 2012). “SdhE Is a Conserved Protein Required for Flavinylation of Succinate Dehydrogenase in Bacteria.” https://doi.org/10.1074/jbc.m111.293803 (mcneil2012sdheisa pages 4-5, mcneil2012sdheisa pages 1-2)
  • Mutyala S. et al. ACS Omega (Jul 2023). “Citrate Synthase Overexpression of Pseudomonas putida Increases Succinate Production from Acetate in Microaerobic Cultivation.” https://doi.org/10.1021/acsomega.3c02520 (mutyala2023citratesynthaseoverexpression pages 10-11)

Scope notes and limitations

  • The retrieved evidence set contained strong strain-specific identity mapping and a 2023 KT2440 expression/regulation signal for sdhA under microaerobic conditions, but did not include KT2440-specific biochemical purification/kinetic constants for SdhA. Therefore, enzyme kinetics and residue-level substrate determinants are not reported here to avoid unsupported extrapolation. (mutyala2023citratesynthaseoverexpression pages 10-11, chavarria2012regulatorytasksof pages 3-4)
  • Where mechanistic details (e.g., SdhE-dependent flavinylation) are drawn from non-P. putida bacterial experiments, they are explicitly framed as conserved bacterial complex II biology rather than KT2440-specific demonstrations. (mcneil2012sdheisa pages 4-5, mcneil2012sdheisa pages 1-2)

References

  1. (chavarria2012regulatorytasksof pages 3-4): Max Chavarría, Roelco J. Kleijn, Uwe Sauer, Katharina Pflüger-Grau, and Víctor de Lorenzo. Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of pseudomonas putida in central carbon metabolism. May 2012. URL: https://doi.org/10.1128/mbio.00028-12, doi:10.1128/mbio.00028-12. This article has 96 citations and is from a domain leading peer-reviewed journal.

  2. (chavarria2012regulatorytasksof media b14b64f4): Max Chavarría, Roelco J. Kleijn, Uwe Sauer, Katharina Pflüger-Grau, and Víctor de Lorenzo. Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of pseudomonas putida in central carbon metabolism. May 2012. URL: https://doi.org/10.1128/mbio.00028-12, doi:10.1128/mbio.00028-12. This article has 96 citations and is from a domain leading peer-reviewed journal.

  3. (chavarria2012regulatorytasksof media 8dabbe7d): Max Chavarría, Roelco J. Kleijn, Uwe Sauer, Katharina Pflüger-Grau, and Víctor de Lorenzo. Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of pseudomonas putida in central carbon metabolism. May 2012. URL: https://doi.org/10.1128/mbio.00028-12, doi:10.1128/mbio.00028-12. This article has 96 citations and is from a domain leading peer-reviewed journal.

  4. (bouillaud2023inhibitionofsuccinate pages 3-5): Frederic Bouillaud. Inhibition of succinate dehydrogenase by pesticides (sdhis) and energy metabolism. International Journal of Molecular Sciences, 24:4045, Feb 2023. URL: https://doi.org/10.3390/ijms24044045, doi:10.3390/ijms24044045. This article has 60 citations.

  5. (mcneil2012sdheisa pages 1-2): Matthew B. McNeil, James S. Clulow, Nabil M. Wilf, George P.C. Salmond, and Peter C. Fineran. Sdhe is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria. Journal of Biological Chemistry, 287:18418-18428, May 2012. URL: https://doi.org/10.1074/jbc.m111.293803, doi:10.1074/jbc.m111.293803. This article has 86 citations and is from a domain leading peer-reviewed journal.

  6. (mcneil2012sdheisa pages 4-5): Matthew B. McNeil, James S. Clulow, Nabil M. Wilf, George P.C. Salmond, and Peter C. Fineran. Sdhe is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria. Journal of Biological Chemistry, 287:18418-18428, May 2012. URL: https://doi.org/10.1074/jbc.m111.293803, doi:10.1074/jbc.m111.293803. This article has 86 citations and is from a domain leading peer-reviewed journal.

  7. (mutyala2023citratesynthaseoverexpression pages 10-11): Sakuntala Mutyala, Shuwei Li, Himanshu Khandelwal, Da Seul Kong, and Jung Rae Kim. Citrate synthase overexpression of pseudomonas putida increases succinate production from acetate in microaerobic cultivation. ACS Omega, 8:26231-26242, Jul 2023. URL: https://doi.org/10.1021/acsomega.3c02520, doi:10.1021/acsomega.3c02520. This article has 13 citations and is from a peer-reviewed journal.

Artifacts

Citations

  1. bouillaud2023inhibitionofsuccinate pages 3-5
  2. mcneil2012sdheisa pages 1-2
  3. mcneil2012sdheisa pages 4-5
  4. mutyala2023citratesynthaseoverexpression pages 10-11
  5. chavarria2012regulatorytasksof pages 3-4
  6. https://doi.org/10.1128/mbio.00028-12
  7. https://doi.org/10.3390/ijms24044045
  8. https://doi.org/10.1074/jbc.m111.293803
  9. https://doi.org/10.1021/acsomega.3c02520
  10. https://doi.org/10.1111/j.1462-2920.2010.02166.x
  11. https://doi.org/10.1128/mbio.00028-12,
  12. https://doi.org/10.3390/ijms24044045,
  13. https://doi.org/10.1074/jbc.m111.293803,
  14. https://doi.org/10.1021/acsomega.3c02520,

📄 View Raw YAML

 
id: Q88FA7
gene_symbol: sdhA
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: Flavoprotein (catalytic) subunit of succinate dehydrogenase (respiratory Complex II) in Pseudomonas putida KT2440. SdhA carries a covalently bound FAD cofactor and the succinate/fumarate active site, catalysing the oxidation of succinate to fumarate with transfer of electrons into the membrane quinone pool (EC 1.3.5.1). This reaction couples the tricarboxylic acid (TCA) cycle to the aerobic respiratory electron transport chain. SdhA forms the soluble catalytic head of the four-subunit enzyme together with the iron-sulfur subunit SdhB (PP_4190) and the membrane anchor subunits SdhD (PP_4192) and SdhC (PP_4193), to which it is peripherally attached on the cytoplasmic face of the inner (plasma) membrane. FAD incorporation (flavinylation) depends on the accessory assembly factor SdhE.
existing_annotations:
- term:
    id: GO:0000104
    label: succinate dehydrogenase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: enables
  review:
    summary: SdhA is the flavoprotein catalytic subunit of succinate dehydrogenase (Complex II); succinate dehydrogenase activity is its core molecular function.
    action: ACCEPT
    reason: Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: SdhA is a peripheral membrane protein attached to the cytoplasmic (inner) face of the inner/plasma membrane as part of the membrane-bound Complex II.
    action: ACCEPT
    reason: Matches UniProt subcellular location (Cell inner membrane; peripheral membrane protein; cytoplasmic side). In Gram-negative bacteria the inner membrane is the GO plasma membrane.
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: Succinate dehydrogenase catalyses the succinate-to-fumarate step of the TCA cycle; this is a core biological process for SdhA.
    action: ACCEPT
    reason: Supported by UniProt pathway annotation (tricarboxylic acid cycle; fumarate from succinate, step 1/1) and conserved enzyme function.
- term:
    id: GO:0008177
    label: succinate dehydrogenase (quinone) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: This is the precise quinone-coupled reaction (succinate + quinone = fumarate + quinol, RHEA:40523, EC 1.3.5.1) catalysed by the holo-enzyme to which SdhA contributes the catalytic flavoprotein head.
    action: ACCEPT
    reason: Directly matches the UniProt CATALYTIC ACTIVITY (RHEA:40523) and EC 1.3.5.1. Most informative molecular-function term for the complex's overall reaction.
- term:
    id: GO:0009055
    label: electron transfer activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: SdhA participates in electron transfer, passing electrons abstracted from succinate via FAD toward the iron-sulfur clusters of SdhB and the quinone pool.
    action: KEEP_AS_NON_CORE
    reason: Biologically true but more generic than the specific succinate dehydrogenase (quinone) activity that captures SdhA's core function. Retain as supporting/non-core rather than primary.
- term:
    id: GO:0009061
    label: anaerobic respiration
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  qualifier: involved_in
  review:
    summary: This subunit is the forward/aerobic succinate dehydrogenase flavoprotein (TIGR01816 sdhA_forward), not the fumarate reductase used in anaerobic respiration.
    action: MARK_AS_OVER_ANNOTATED
    reason: UniProt notes that two distinct FAD enzymes interconvert fumarate and succinate, with fumarate reductase (FrdA) used in anaerobic growth and succinate dehydrogenase used in aerobic growth. The forward SdhA is assigned to aerobic respiration; this TreeGrafter-propagated anaerobic respiration term reflects the broader SdhA/FrdA family and over-annotates the aerobic SdhA.
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Generic parent of the specific succinate dehydrogenase (quinone) activity already annotated.
    action: KEEP_AS_NON_CORE
    reason: Correct but uninformative high-level term; subsumed by the specific EC 1.3.5.1 annotation. Retain as non-core.
- term:
    id: GO:0016627
    label: oxidoreductase activity, acting on the CH-CH group of donors
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Accurate intermediate-level description of the chemistry (oxidation of the succinate CH-CH bond to the fumarate C=C bond), but less specific than succinate dehydrogenase (quinone) activity.
    action: KEEP_AS_NON_CORE
    reason: Correct grouping term but subsumed by the specific MF term; keep as non-core supporting annotation.
- term:
    id: GO:0022900
    label: electron transport chain
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: involved_in
  review:
    summary: Complex II feeds electrons from succinate into the respiratory quinone pool, contributing to the aerobic electron transport chain.
    action: ACCEPT
    reason: Supported by UniProt (electron transport keyword) and the established role of Complex II linking the TCA cycle to respiration.
- term:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: SdhA binds a (covalently attached) FAD cofactor essential for succinate oxidation.
    action: ACCEPT
    reason: Supported by UniProt COFACTOR (FAD), multiple conserved FAD-binding residues, the Tele-8alpha-FAD histidine modified residue, and SdhE-dependent flavinylation.
- term:
    id: GO:0160308
    label: succinate dehydrogenase (FAD) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: Describes the FAD-dependent succinate->fumarate half-reaction occurring at the SdhA flavin site, prior to electron transfer to quinone.
    action: ACCEPT
    reason: Accurately captures the FAD-coupled catalytic step intrinsic to the SdhA subunit; complementary to the holo-enzyme quinone-coupled term GO:0008177. Both are valid and informative.
core_functions:
- description: Catalytic flavoprotein subunit of succinate dehydrogenase (Complex II) that oxidises succinate to fumarate using a covalently bound FAD cofactor, the rate-limiting catalytic step linking the TCA cycle to the respiratory chain.
  molecular_function:
    id: GO:0008177
    label: succinate dehydrogenase (quinone) activity
  supported_by:
  - reference_id: GO_REF:0000120
    supporting_text: UniProt CATALYTIC ACTIVITY a quinone + succinate = fumarate + a quinol (RHEA:40523, EC 1.3.5.1).
  directly_involved_in:
  - id: GO:0006099
    label: tricarboxylic acid cycle
- description: Binds FAD at the catalytic head to abstract electrons from succinate and feed them into the electron transport chain via the SdhB iron-sulfur clusters and the membrane quinone pool.
  molecular_function:
    id: GO:0050660
    label: flavin adenine dinucleotide binding
  directly_involved_in:
  - id: GO:0022900
    label: electron transport chain
  supported_by:
  - reference_id: GO_REF:0000120
    supporting_text: UniProt COFACTOR FAD; conserved FAD-binding residues and Tele-8alpha-FAD histidine.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:22474332
  title: SdhE is a conserved protein required for flavinylation of succinate dehydrogenase in bacteria
  findings:
  - statement: The accessory protein SdhE binds FAD and is required for flavinylation of the succinate dehydrogenase flavoprotein subunit (SdhA) and for SDH activity in bacteria.
    reference_section_type: RESULTS
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: McNeil et al., J Biol Chem 2012;287:18418-28 (Serratia); supports SdhE-dependent flavinylation of bacterial SdhA. PMID corrected from 22593091 (which resolves to an unrelated orthopedics paper) to 22474332, recovered via DOI 10.1074/jbc.M111.293803 and PubMed-verified to the intended SdhE paper.
suggested_questions:
- question: Has the SdhA-SdhBCD Complex II of P. putida KT2440 been biochemically characterised (kinetics, FAD content, quinone specificity), and does it show any fumarate reductase activity in vitro?
suggested_experiments:
- description: Purify the P. putida KT2440 SdhABCD complex and measure succinate:quinone oxidoreductase kinetics and FAD flavinylation status, with and without SdhE, to confirm the conserved mechanism in this organism.