Curation Notes for ssuA2 (VPARA_09270, A0A0H2M784) in Variovorax paradoxus TBEA6

1. Gene & Protein Overview

• UniProtKB Accession: A0A0H2M784 (A0A0H2M784_VARPD, unreviewed, 319 aa, 33,241 Da)
• Gene Symbol / Locus Tag: ssuA2 / VPARA_09270 (EMBL:KLN57916.1 on genomic contig JZWI01000005, RefSeq:WP_021006431.1)
• Organism: Variovorax paradoxus strain TBEA6 (NCBITaxon:34073)
• Genomic Context: Encoded on contig JZWI01000005 within the aliphatic sulfonate uptake and desulfonation gene cluster spanning ssuB2 (VPARA_09230, KLN57912.1), ssuC5 (VPARA_09240, KLN57913.1), ssuD (VPARA_09250, KLN57914.1), ssuA2 (VPARA_09270, KLN57916.1), and ssuE (VPARA_09290, KLN57918.1).
• Domain Architecture & Targeting:
• N-terminal Twin-arginine translocation (Tat) signal peptide (PROSITE:PS51318, residues 1..29, 1-MTSISVPRRRLLQGAAAAAIALPSFAALA-29) containing the canonical twin-arginine motif Arg8-Arg9-Arg10 (8-RRRLLQ-13), directing export of the folded precursor across the inner membrane into the periplasm.
• Mature periplasmic substrate-binding domain (residues 30..319): NCBIfam:TIGR01728 (ssuA, aliphatic sulfonates-binding protein), InterPro:IPR010067 (Aliphatic_sulfonates-bd_SsuA), PANTHER:PTHR30024:SF42 (ALIPHATIC SULFONATES-BINDING PROTEIN-RELATED), and periplasmic binding protein-like II superfamily (InterPro:IPR028082, SUPFAM:SSF53850).

2. Literature & Comparative Evidence

• PMID:10781534(https://pubmed.ncbi.nlm.nih.gov/10781534/) (Eichhorn, van der Ploeg & Leisinger 2000, J Bacteriol 182:2687-2695): Deletion and complementation analysis of the Escherichia coli tauABCD and ssuEADCB gene clusters established that SsuABC forms a dedicated ABC-type uptake system for aliphatic sulfonates that is functionally distinct from and non-exchangeable with TauABC ("the individual components of the two transport systems were not functionally exchangeable").
• PMID:10781557(https://pubmed.ncbi.nlm.nih.gov/10781557/) (Kahnert et al. 2000, J Bacteriol 182:2869-2878): Characterized the ssuEADCBF operon in Pseudomonas putida S-313, identifying ssuA, ssuB, and ssuC as the periplasmic binding, ATP-binding, and membrane permease subunits of the ABC-type sulfonate importer supplying the SsuED monooxygenase system ("The first group consists of ssuA , ssuB , and ssuC , which are the genes for a putative ATP-binding cassette (ABC)-type transport system.").

3. Review of Existing GOA Annotations (4 IEA rows)

1. GO:0016020 (membrane, located_in, IEA GO_REF:0000002 from InterPro:IPR010067) -> REMOVE:
2. Incorrect InterPro2GO propagation (WRONG_TERM / SCOPE_OVER_REACH) from InterPro:IPR010067 (ABC_SsuA_sub-bd); mature SsuA2 (residues 30..319) is a soluble periplasmic solute-binding protein lacking transmembrane helices, localizing to GO:0030288 (outer membrane-bounded periplasmic space).
3. GO:0042597 (periplasmic space, located_in, IEA GO_REF:0000044 from UniProtKB-SubCell:SL-0200) -> MODIFY to GO:0030288 (outer membrane-bounded periplasmic space):
4. Refined to GO:0030288 (outer membrane-bounded periplasmic space) for this diderm Gram-negative betaproteobacterial periplasmic binding protein following cleavage of the N-terminal Tat signal peptide (residues 1..29, PROSITE:PS51318).
5. GO:0042626 (ATPase-coupled transmembrane transporter activity, enables, IEA GO_REF:0000002 from InterPro:IPR010067) -> MARK_AS_OVER_ANNOTATED:
6. GO:0042626 describes the ATP-driven transmembrane transport activity of the intact SsuABC complex (GO:0055052) rather than the soluble periplasmic substrate-binding subunit SsuA2 alone. Its complex-level contribution is recorded via contributes_to_molecular_function (GO:0042959) in core_functions.
7. GO:0055085 (transmembrane transport, involved_in, IEA GO_REF:0000108 from GO:0042626) -> MODIFY to GO:0042918 (alkanesulfonate transmembrane transport):
8. Refined to GO:0042918 (alkanesulfonate transmembrane transport) based on NCBIfam:TIGR01728, PANTHER:PTHR30024:SF42, and syntenic clustering in the ssuB2-ssuC5-ssuD-...-ssuA2-...-ssuE locus (UniProtKB:A0A0H2MBB8, UniProtKB:A0A0H2M6G6, UniProtKB:A0A0H2MCI3, UniProtKB:A0A0H2M6H0).

4. Proposed New Annotations

• GO:0055052 (ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing, part_of, IC from file:VARPD/ssuA2/ssuA2-uniprot.txt and PMID:10781557) -> NEW:
• SsuA2 (VPARA_09270, EMBL:KLN57916.1) is encoded in the same contig JZWI01000005 cluster as the ATPase subunit ssuB2 (VPARA_09230, UniProtKB:A0A0H2MBB8, KLN57912.1) and the permease subunit ssuC5 (VPARA_09240, UniProtKB:A0A0H2M6G6, KLN57913.1), assembling into the substrate-binding-subunit-containing ABC importer complex (GO:0055052).