Role of <scp>C</scp>a<sup>2+</sup> in folding the tandem β‐sandwich extender domains of a bacterial ice‐binding adhesin

Guo, Shuaiqi; Garnham, Christopher P.; Partha, Sarathy Karunan; Campbell, Robert L.; Allingham, John S.; Davies, Peter L.

doi:10.1111/febs.12518

Cited by 23 publications

(36 citation statements)

References 48 publications

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“…We have previously shown that the RII-tandemer is fully structured in 10 molar equivalents of Ca 2+ but resembles a random coil in the absence of this ion [12]. Similar analyses were applied to the RII tetra-tandemer.…”

Section: Resultsmentioning

confidence: 91%

“…The lipopolysaccharide layer also confers to the bacterial outer membrane an overall negative charge. Mp AFP_RII is rich in negatively charged acidic residues (18% Asp+Glu), and contains no Lys or Arg [12]. The acidic residues of RII not only help coordinate Ca 2+ to stabilize the protein's fold, but also may be repelled from the negatively charged cell surface for better extension of the ice-binding domain.…”

Section: Discussionmentioning

confidence: 99%

“…Mp AFP_RII protomers require roughly 10 molar equivalents of Ca 2+ to be fully structured [12]. The ice-binding RIV also requires the presence of millimolar Ca 2+ for folding.…”

Section: Discussionmentioning

confidence: 99%

“…Data were collected at the X6A beamline of the National Synchrotron Light Source (Brookhaven National Laboratory) and were indexed and integrated with XDS [14], and scaled with CCP4-Aimless [15,16]. The structure was solved by molecular replacement with CCP4-Phaser [16,17], using the RII-tandemer structure as the search model (PDB: 4KDV) [12]. The initial model of the RII tetra-tandemer was built using CCP4-Buccaneer [16,18] and was manually corrected in Coot [19].…”

Section: Methodsmentioning

confidence: 99%

“…RII consists of approximately 120 tandem copies of a perfect 104-aa repeat that account for over 90% of the mass of the 1.5-MDa protein. We recently solved the X-ray crystal structure of a single 104-aa RII repeat (referred to here as a tandemer) to 1.35-Å resolution [12]. The RII-tandemer is a BIg (bacterial immunoglobulin)-like beta-sandwich domain that requires at least three Ca 2+ ions for folding.…”

Section: Introductionmentioning

confidence: 99%

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Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

et al. 2014

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The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

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Section: Resultsmentioning

confidence: 91%

Section: Discussionmentioning

confidence: 99%

“…Mp AFP_RII protomers require roughly 10 molar equivalents of Ca 2+ to be fully structured [12]. The ice-binding RIV also requires the presence of millimolar Ca 2+ for folding.…”

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

et al. 2014

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Similarity between the Usher Plug and the Repeating Domain of an Ice‐adhesin: Evolution via Surface Reshaping

Kessel

Kolodny

Ben‐Tal

2017

Israel Journal of Chemistry

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The PapC usher and MpAFP ice‐adhesin feature Ig‐like domains, which are similar in shape and sequence but are engaged in very different functions. We explore how evolution reshaped the surfaces of these two domains to fit to their respective functions. In PapC, the Ig‐like domain forms a rigid plug that seals the translocation channel in the inactive state. Upon activation, it undergoes a hinge motion, as an intact domain, to allow passage and assembly of the pili that goes through the pore. In accordance with this function, our calculations show that its surface is, in essence, electrostatically neutral, to facilitate the interaction with the PapC pore, and that this feature is evolutionarily conserved among its close homologues. On the other hand, within the context of MpAFP, the Ig‐like domain is the main repeating unit, and our calculations show that its surface features a negative electrostatic potential of unusually high magnitude. The potential is balanced by bound Ca2+ ions. This is consistent with Ca2+‐dependent secretion of unfolded MpAFP across the double membrane of the bacterium, and folding outside, where Ca2+ concentration is high.

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Adhesin domains responsible for binding bacteria to surfaces they colonize project outwards from companion split domains

Graham,

Hansen,

Yang

et al. 2024

Proteins

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Bacterial adhesins attach their hosts to surfaces that the bacteria will colonize. This surface adhesion occurs through specific ligand‐binding domains located towards the distal end of the long adhesin molecules. However, recognizing which of the many adhesin domains are structural and which are ligand binding has been difficult up to now. Here we have used the protein structure modeling program AlphaFold2 to predict structures for these giant 0.2‐ to 1.5‐megadalton proteins. Crystal structures previously solved for several adhesin regions are in good agreement with the models. Whereas most adhesin domains are linked in a linear fashion through their N‐ and C‐terminal ends, ligand‐binding domains can be recognized by budding out from a companion core domain so that their ligand‐binding sites are projected away from the axis of the adhesin for maximal exposure to their targets. These companion domains are “split” in their continuity by projecting the ligand‐binding domain outwards. The “split domains” are mostly β‐sandwich extender modules, but other domains like a β‐solenoid can serve the same function. Bioinformatic analyses of Gram‐negative bacterial sequences revealed wide variety ligand‐binding domains are used in their Repeats‐in‐Toxin adhesins. The ligands for many of these domains have yet to be identified but known ligands include various cell‐surface glycans, proteins, and even ice. Recognizing the ligands to which the adhesins bind could lead to ways of blocking colonization by bacterial pathogens. Engineering different ligand‐binding domains into an adhesin has the potential to change the surfaces to which bacteria bind.

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Role of Ca²⁺ in folding the tandem β‐sandwich extender domains of a bacterial ice‐binding adhesin

Cited by 23 publications

References 48 publications

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

Similarity between the Usher Plug and the Repeating Domain of an Ice‐adhesin: Evolution via Surface Reshaping

Adhesin domains responsible for binding bacteria to surfaces they colonize project outwards from companion split domains

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Role of Ca2+ in folding the tandem β‐sandwich extender domains of a bacterial ice‐binding adhesin

Cited by 23 publications

References 48 publications

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

Similarity between the Usher Plug and the Repeating Domain of an Ice‐adhesin: Evolution via Surface Reshaping

Adhesin domains responsible for binding bacteria to surfaces they colonize project outwards from companion split domains

Contact Info

Product

Resources

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Role of Ca²⁺ in folding the tandem β‐sandwich extender domains of a bacterial ice‐binding adhesin