sdhB

UniProt ID: Q88FA8
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
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Gene Description

Iron-sulfur subunit of the membrane-bound succinate dehydrogenase/respiratory Complex II enzyme in Pseudomonas putida KT2440. SdhB transfers electrons from the SdhA flavoprotein catalytic subunit through iron-sulfur clusters toward the membrane anchor/quinone site, contributing to quinone-linked succinate oxidation. This places SdhB at the interface between the tricarboxylic acid cycle and the aerobic respiratory electron transport chain.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006099 tricarboxylic acid cycle
IEA
GO_REF:0000002
ACCEPT
Summary: Correct process annotation for the succinate-to-fumarate step of the TCA cycle.
Reason: SdhB is part of the succinate dehydrogenase complex that oxidizes succinate to fumarate in the TCA cycle. The support is family classification, not direct P. putida data -- NCBIfam TIGR00384 (dhsB) and PANTHER PTHR11921:SF29 place Q88FA8 in the succinate dehydrogenase iron-sulfur subunit subfamily, whose members act in the TCA-cycle succinate-to-fumarate step as part of SdhABCD. (The UniProt PATHWAY line is ARBA-only and is not cited.) A provider pathway report also places the sdhCDAB operon at this step, as context only.
Supporting Evidence:
file:PSEPK/sdhB/sdhB-uniprot.txt
PANTHER; PTHR11921:SF29; SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL
file:PSEPK/sdhB/sdhB-uniprot.txt
NCBIfam; TIGR00384; dhsB; 1.
GO:0008177 succinate dehydrogenase (quinone) activity
IEA
GO_REF:0000120
ACCEPT
Summary: Correct holoenzyme activity that SdhB contributes to as the iron-sulfur electron-transfer subunit.
Reason: The complete SdhABCD complex catalyzes quinone-linked succinate oxidation (EC 1.3.5.1). SdhB contributes electron transfer within this complex rather than carrying the flavin active site independently. Support is family membership -- PANTHER PTHR11921 (succinate dehydrogenase iron-sulfur protein) and its SF29 succinate dehydrogenase [ubiquinone] subfamily, plus InterPro IPR004489 -- whose members are the Fe-S subunit of succinate:quinone oxidoreductase; the UniProt CATALYTIC ACTIVITY line is ARBA-only and is not cited.
Supporting Evidence:
file:PSEPK/sdhB/sdhB-uniprot.txt
PANTHER; PTHR11921:SF29; SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL
file:PSEPK/sdhB/sdhB-uniprot.txt
InterPro; IPR004489; Succ_DH/fum_Rdtase_Fe-S.
GO:0009055 electron transfer activity
IEA
GO_REF:0000002
ACCEPT
Summary: Correct and subunit-relevant function for the SdhB iron-sulfur protein.
Reason: SdhB is the iron-sulfur relay between the SdhA flavoprotein site and the membrane quinone-reduction site, so electron transfer is a meaningful subunit-level function.
GO:0009060 aerobic respiration
IEA
GO_REF:0000118
ACCEPT
Summary: Correct respiratory-process context for forward succinate dehydrogenase/Complex II.
Reason: Within the SDH/FRD iron-sulfur protein family, PANTHER places Q88FA8 in the succinate dehydrogenase [ubiquinone] subfamily (SF29) rather than with the fumarate reductases that serve anaerobic respiration, and P. putida KT2440 is a strictly aerobic bacterium, so the complex acts in aerobic respiratory electron transfer. This is a family-level argument; the UniProt FUNCTION text on aerobic vs anaerobic use is ARBA-only and is not cited.
Supporting Evidence:
file:PSEPK/sdhB/sdhB-uniprot.txt
PANTHER; PTHR11921:SF29; SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002
KEEP AS NON CORE
Summary: Correct but broad parent of the specific succinate dehydrogenase/electron-transfer role.
Reason: The SdhB-containing complex is an oxidoreductase, but GO:0008177 and GO:0009055 better capture the specific complex-level and subunit-level functions.
GO:0022904 respiratory electron transport chain
IEA
GO_REF:0000118
ACCEPT
Summary: Correct process annotation because Complex II feeds electrons from succinate into the quinone pool.
Reason: SdhB is an electron-transfer subunit of respiratory Complex II. The complex bridges TCA-cycle succinate oxidation to the respiratory electron transport chain.
GO:0051536 iron-sulfur cluster binding
IEA
GO_REF:0000002
ACCEPT
Summary: Correct cofactor-binding annotation for the succinate dehydrogenase iron-sulfur subunit.
Reason: SdhB carries an N-terminal plant-type [2Fe-2S] ferredoxin-like domain (Pfam PF13085 Fer2_3) and a C-terminal helical ferredoxin domain with a 4Fe-4S ferredoxin-type signature (PROSITE PS00198/PS51379), consistent with the [2Fe-2S], [4Fe-4S] and [3Fe-4S] clusters of SDH iron-sulfur subunits. Because it binds clusters of several types, the general iron-sulfur cluster binding term is appropriate. Support is domain classification; the UniProt COFACTOR lines are ARBA-only and are not cited. Iron-sulfur cluster binding is intrinsic to SdhB electron transfer.
Supporting Evidence:
file:PSEPK/sdhB/sdhB-uniprot.txt
Pfam; PF13085; Fer2_3; 1.
file:PSEPK/sdhB/sdhB-uniprot.txt
PROSITE; PS00198; 4FE4S_FER_1; 1.

Core Functions

Iron-sulfur electron-transfer subunit of succinate dehydrogenase/Complex II, relaying electrons from succinate oxidation through Fe-S clusters toward quinone reduction by the SdhABCD complex.

Supporting Evidence:
  • file:PSEPK/sdhB/sdhB-uniprot.txt
    PANTHER; PTHR11921:SF29; SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR SUBUNIT, MITOCHONDRIAL
  • file:PSEPK/sdhB/sdhB-uniprot.txt
    NCBIfam; TIGR00384; dhsB; 1.
  • file:PSEPK/sdhB/sdhB-uniprot.txt
    Pfam; PF13085; Fer2_3; 1.

References

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Suggested Questions for Experts

Q: What are the quinone specificity and electron-transfer kinetics of the P. putida KT2440 SdhABCD complex?

Suggested Experiments

Experiment: Purify SdhABCD and assay succinate-dependent reduction of physiological and analog quinones, while mutating conserved SdhB Fe-S ligands to confirm the electron-transfer path.

Deep Research

OpenScientist

(sdhB-deep-research-openscientist.md)

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πŸ“š Additional Documentation

Notes

(sdhB-notes.md)

sdhB notes

OpenScientist adjudication

The sdhB OpenScientist report identified Q88FA8/PP_4190 as the Complex II
iron-sulfur subunit and explicitly noted that no P. putida-specific
biochemical study of SdhB was retrieved. I used it as corroborating context for
the conserved SdhB/SdhA/SdhC/SdhD architecture rather than as direct
P. putida KT2440 enzymology.

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