SdbA (Scaffolding dockerin binding protein A) is an anchoring scaffoldin in the Acetivibrio thermocellus (formerly Clostridium thermocellum) cellulosome system. It is a non-catalytic cell surface protein that functions to tether the primary scaffoldin CipA (and its associated enzyme complement) to the bacterial cell envelope. SdbA contains a single type II cohesin domain that specifically binds the C-terminal type II dockerin (XDocII) of CipA, and three SLH (S-layer homology) domains that mediate attachment to the peptidoglycan/cell wall. Unlike cellulosomal enzymes, SdbA has NO catalytic activity and does NOT bind carbohydrates directly - its function is purely structural/scaffolding. Genetic deletion studies show that sdbA mutants have moderate (14-25%) reductions in cellulose hydrolysis, indicating functional redundancy with other anchoring scaffoldins (OlpB, Orf2p).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000272 polysaccharide catabolic process | IEA GO_REF:0000002 | REMOVE | Summary: This annotation is INCORRECT. SdbA is a non-catalytic anchoring scaffoldin that does NOT participate in polysaccharide catabolism. The protein lacks any glycosyl hydrolase domains or catalytic activity. The InterPro mapping from the cohesin domain (IPR002102) is erroneous - cohesin domains mediate protein-protein interactions with dockerin domains, not carbohydrate degradation. The deep research confirms that SdbA is best annotated as a noncatalytic, cell-surface anchoring scaffoldin. Reason: SdbA contains a type II cohesin domain that binds dockerin, not carbohydrates or polysaccharides. The protein has no enzymatic activity whatsoever. It functions solely as a structural adaptor to tether cellulosomes to the cell surface via SLH-mediated cell envelope binding. The annotation derives from an incorrect InterPro2GO mapping that conflates structural similarity between cohesin and CBM domains with functional similarity. Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md SdbA is best annotated as a noncatalytic, cell-surface anchoring scaffoldin with a single type II cohesin and SLH repeats, mediating attachment of CipA-based cellulosomes to the cell envelope |
| GO:0005576 extracellular region | IEA GO_REF:0000044 | MODIFY | Summary: This annotation is correct but overly broad. SdbA is indeed secreted and localized extracellularly, but it is specifically anchored to the cell surface via its SLH domains. The UniProt subcellular location annotation Secreted supports this, though GO:0009986 (cell surface) would be more specific given the SLH-mediated cell envelope attachment. Reason: While technically correct that SdbA is in the extracellular region, this term is too general. SdbA is specifically tethered to the cell surface via its three SLH domains which bind cell envelope components (peptidoglycan). The protein does not freely diffuse in the extracellular space but is surface- associated. A more accurate annotation would reflect its cell surface localization. Proposed replacements: cell surface Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md SdbA contains SLH repeats that bind cell envelope components, providing noncovalent anchoring to the bacterial surface |
| GO:0030246 carbohydrate binding | IEA GO_REF:0000002 | MODIFY | Summary: This annotation is INCORRECT. SdbA does NOT bind carbohydrates. The type II cohesin domain binds the type II dockerin domain of CipA (a protein-protein interaction), not carbohydrates. This erroneous annotation stems from the InterPro mapping of cohesin domains (IPR002102) and the CBM superfamily (IPR008965), which share structural similarity but have completely different functions. Cohesin-dockerin interactions are protein-protein, calcium-dependent binding events, not carbohydrate binding. Reason: SdbA cohesin domain specifically binds the dockerin domain of CipA scaffoldin - this is a well-characterized protein-protein interaction, not carbohydrate binding. The structural similarity between cohesin domains and CBM domains (both belong to beta-sandwich fold families) has led to erroneous functional annotation. The correct molecular function is type-II dockerin domain binding, which accurately describes SdbA role in capturing CipA for cell surface anchoring. Proposed replacements: type-II dockerin domain binding Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md The type II dockerin from CipA binds specifically to type II cohesins on SdbA ... type II interactions mediate scaffoldin-scaffoldin and anchoring to the cell surface |
| GO:0044575 cellulosome assembly | TAS PMID:24955112 The contribution of cellulosomal scaffoldins to cellulose hy... | NEW | Summary: SdbA plays a direct role in cellulosome assembly by providing an anchoring point for the CipA scaffoldin at the cell surface. While SdbA does not participate in the type I cohesin-dockerin interactions that recruit enzymes to CipA, it is essential for the final step of cellulosome architecture: tethering the assembled complex to the cell. Genetic studies show that deletion of anchoring scaffoldins affects cellulosome display. Reason: This annotation captures SdbA role in the biological process of organizing the cellulosome at the cell surface. The protein is part of the multi-protein anchoring system that completes cellulosome architecture. Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md SdbA single type II cohesin provides one docking site for CipA, complementing multi-cohesin anchoring scaffoldins to generate polycellulosomes of varying sizes at the cell surface PMID:24955112 Disruptants lacking any of four different secondary scaffoldins (OlpB, 7CohII, Orf2p, or SdbA) showed moderately decreased cellulose hydrolysis rates, suggesting additive contributions |
| GO:1990309 type-II dockerin domain binding | IDA PMID:8655483 A new type of cohesin domain that specifically binds the doc... | NEW | Summary: This is the core molecular function of SdbA. The type II cohesin domain specifically recognizes and binds the C-terminal type II dockerin (XDocII) of CipA scaffoldin. This interaction is calcium-dependent and has been characterized structurally by X-ray crystallography (PDB: 2BM3, 4FL4). Reason: This term precisely describes SdbA molecular function. The protein cohesin domain binds dockerin domains, not carbohydrates. This is a well- characterized, high-affinity protein-protein interaction that has been validated structurally and biochemically. Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md SdbA is a cell-surface anchoring scaffoldin that tethers CipA-based cellulosomes to the bacterial envelope via high-affinity binding between CipA C-terminal type II dockerin (XDocII) and the SdbA type II cohesin PMID:8655483 The NH2-terminal region of SdbA and a fusion protein carrying the first NH2-terminal repeat of OlpB were shown to bind the dockerin domain of CipA |
| GO:0009986 cell surface | IDA PMID:24955112 The contribution of cellulosomal scaffoldins to cellulose hy... | NEW | Summary: SdbA is localized to the cell surface via its three SLH (S-layer homology) domains which bind noncovalently to peptidoglycan/cell envelope components. This positions the type II cohesin domain extracellularly to capture CipA. Proteomics studies detect SdbA in cell-associated cellulosome fractions. Reason: This annotation accurately reflects SdbA cellular localization as determined by biochemical studies showing it is tethered to the cell surface via SLH domain interactions with the cell wall. Supporting Evidence: file:ACET2/P71143/P71143-deep-research-falcon.md SdbA was detected in cell-associated cellulosomes ... SLH-mediated cell-envelope binding of anchoring scaffoldins is supported biochemically PMID:24955112 attached to the cell surface by non-catalytic scaffoldins |
Loading supporting content…
Download this section (compressed HTML)Q: What is the precise binding affinity (Kd) of SdbA cohesin for CipA XDocII dockerin?
Q: How do the three SLH domains of SdbA cooperate in cell wall attachment?
Q: What is the stoichiometry of anchoring scaffoldins (SdbA/OlpB/Orf2p) on the cell surface?
Experiment: Surface plasmon resonance or ITC to quantify SdbA-CipA binding kinetics
Hypothesis: SdbA cohesin binds CipA dockerin with nanomolar affinity
Experiment: Mutagenesis of individual SLH domains to assess their relative contributions to anchoring
Hypothesis: All three SLH domains contribute to stable cell wall attachment
Experiment: Quantitative proteomics of cell-surface vs secreted cellulosome fractions in different media
Hypothesis: Growth conditions affect the ratio of anchored vs free cellulosomes
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)