The Prolyl Isomerase SlyD Is a Highly Efficient Enzyme but Decelerates the Conformational Folding of a Client Protein

Geitner, Anne-Juliane; Schmid, Franz X.

doi:10.1021/ja311775a

Cited by 6 publications

(11 citation statements)

References 47 publications

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“…SlyD-like or FKBP-IF proteins are structurally − well characterized, and their assumed relationship between intrinsic dynamics and enzymatic activity has been reported in great detail − and recently reviewed . A synergistic interplay between both domains of SlyD is suggested to be crucial for increasing the PPIase activity for protein substrates by 2 orders of magnitude compared to that of single domain h FKBP12. , This dynamic cooperation involves a high interaction probability and rapid binding by the IF domain of a broad range of unfolded and aggregation-prone proteins and signal peptides. ,,, …”

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confidence: 99%

Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli

et al. 2017

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SlpA (SlyD-like protein A) comprises two domains, a FK506 binding domain (FKBP fold) of moderate prolyl cis/trans-isomerase activity and an inserted in flap (IF) domain that hosts its chaperone activity. Here we present the nuclear magnetic resonance (NMR) solution structure of apo Escherichia coli SlpA determined by NMR that mirrors the structural properties seen for various SlyD homologues. Crucial structural differences in side-chain orientation arise for F37, which points directly into the hydrophobic core of the active site. It forms a prominent aromatic stacking with F15, one of the key residues for PPIase activity, thus giving a possible explanation for the inherently low PPIase activity of SlpA. The IF domain reveals the highest stability within the FKBP-IF protein family, most likely arising from an aromatic cluster formed by four phenylalanine residues. Both the thermodynamic stability and the PPIase and chaperone activity let us speculate that SlpA is a backup system for homologous bacterial systems under unfavorable conditions.

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confidence: 99%

Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli

et al. 2017

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“…The presence of SlyD accelerates isomerization dramatically, which makes the evaluation of eight different interconnected fast rate constants quite challenging. Previously, Žoldák et al showed from stopped flow experiments, at 7.25 μM concentration, the SlyD binding rate is 174 s –1 and dissociation rate is 25 s –1 . The catalyzed isomerization kinetics was reported on the order of 100 s –1 , which indicates that a catalyzed back-and-forth isomerization would happen on the order of 10 ms.…”

Section: Discussionmentioning

confidence: 94%

“…In one such study, Žoldák et al reported an FKBP enzyme that catalyzes conformational folding of ribonuclease T1 protein. They observed an ∼10 4 times accelerated prolyl cis–trans isomerization rate in the presence of the enzyme SlyD. , …”

Section: Introductionmentioning

confidence: 97%

SlyD Accelerates trans-to-cis Prolyl Isomerization in a Mechanosignaling Protein under Load

et al. 2021

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Prolyl isomerization is recognized as one of the key regulatory mechanisms, which plays a crucial role in cell signaling, ion channel gating, phage virus infection, and molecular timing. This isomerization is usually slow but often accelerated by an enzyme, called peptidyl−prolyl isomerase (PPIase). In the current project, we investigate using single-molecule force spectroscopy (SMFS) the impact of a bacterial PPIase, SlyD, on the cis−trans isomerization of the proline 2225 (P2225) in an isolated 20th domain of a cytoskeletal mechanosensing protein filamin-A (FlnA20). To explore the FlnA20−PPIase interaction, we have used multiple SMFS modes, like constant velocity, constant distance, and jumping trap experiments. In our previous study, we reported the unique nature of the P2225, which is conserved in all naturally occurring filamins and can slowly (minutes) interconvert between cis−trans isomers, in absence of any PPIase. Our current results show a staggering 25-fold acceleration of the trans-to-cis isomerization rate in the presence of saturating SlyD concentration (7.25 μM) compared to the unenzymatic condition. A SlyD concentration-dependent depletion of the trans isomeric lifetime was also observed. Additionally, we observed that SlyD stabilizes the cis-isomer in the native state of FlnA20 by ∼2 k B T. This is the first single-molecule observation of the cis−trans isomerization catalysis by a PPIase in a mechanosensing protein.

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“…(A) Crude extracts derived from strains MC4100, CP870 (DslyD) and CP870 transformed with pBADslyD, grown anaerobically in TGYEP, pH 6.5 in the presence of L-Ara as indicated until exponential (exp.) 30 The recovery of dye-reducing activity of all three hydrogenases by increasing the copy-number of the slyD gene in late-stationary phase, without the necessity to add nickel ions to the culture medium, indicates that nickel per se is not limiting under these growth conditions. phase, were prepared.…”

Section: H 2 Accumulates In Cultures Of a Strain Lacking Slydmentioning

confidence: 99%

“…This might be related to the ability of the prolyl isomerase function of SlyD to affect negatively protein folding. 30 The recovery of dye-reducing activity of all three hydrogenases by increasing the copy-number of the slyD gene in late-stationary phase, without the necessity to add nickel ions to the culture medium, indicates that nickel per se is not limiting under these growth conditions. Rather, these data support the hypothesis 12,13 that SlyD is a nickel reservoir, which delivers the ion to HypB for insertion into the active site.…”

Section: H 2 Accumulates In Cultures Of a Strain Lacking Slydmentioning

confidence: 99%

SlyD-dependent nickel delivery limits maturation of [NiFe]-hydrogenases in late-stationary phase Escherichia coli cells

2015

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Fermentatively growing Escherichia coli cells have three active [NiFe]-hydrogenases (Hyd), two of which, Hyd-1 and Hyd-2, contribute to H2 oxidation while Hyd-3 couples formate oxidation to H2 evolution. Biosynthesis of all Hyd involves the insertion of a Fe(CN)2CO group and a subsequent insertion of nickel ions through the HypA/HybF, HypB and SlyD proteins. With high nickel concentrations the presence of none of these proteins is required, but under normal growth conditions and during late stationary growth SlyD is important for hydrogenase activities. The slyD mutation reduced H2 production during exponential phase growth by about 50%. Assaying stationary phase grown cells for the coupling of Hyd activity to the respiratory chain or formate-dependent H2 evolution showed that SlyD is essential for both H2 evolution and H2 oxidation. Although introduction of plasmid-coded slyD resulted in an overall decrease of Hyd-2 polypeptides in slyD and hypA slyD mutants, processing and dye-reducing activity of the Hyd-2 enzyme was nevertheless restored. Similarly, introduction of the slyD plasmid restored only some H2 evolution in the slyD mutant while Hyd-3 polypeptides and dye-reducing activity were fully restored. Taken together, these results indicate an essential role for SlyD in the generation of the fully cofactor-equipped hydrogenase large subunits in the stationary phase where the level of each Hyd enzyme is finely tuned by SlyD for optimal enzyme activity.

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The Prolyl Isomerase SlyD Is a Highly Efficient Enzyme but Decelerates the Conformational Folding of a Client Protein

Cited by 6 publications

References 47 publications

Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli

Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli

SlyD Accelerates trans-to-cis Prolyl Isomerization in a Mechanosignaling Protein under Load

SlyD-dependent nickel delivery limits maturation of [NiFe]-hydrogenases in late-stationary phase Escherichia coli cells

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