NMR Solution Structure of SlyD from Escherichia coli: Spatial Separation of Prolyl Isomerase and Chaperone Function

Weininger, Ulrich; Haupt, Caroline; Schweimer, Kristian; Graubner, Wenke; Kovermann, Michael; Brüser, Thomas; Schölz, Christian; Schaarschmidt, Peter; Žoldák, Gabriel; Schmid, Franz X.; Balbach, Jochen

doi:10.1016/j.jmb.2009.01.034

Cited by 72 publications

(178 citation statements)

References 44 publications

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“…This assay was validated for all three families of prolyl isomerases. 46 The prolyl isomerases SlyD [47][48][49] and cyclophi- could not accelerate this reaction [ Fig. 5(A)].…”

Section: Ppid* Does Not Catalyze Prolyl Isomerization In Peptides or mentioning

confidence: 99%

The prolyl isomerase domain of PpiD fromEscherichia colishows a parvulin fold but is devoid of catalytic activity

et al. 2009

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PpiD is a periplasmic folding helper protein of Escherichia coli. It consists of an N-terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264-357) shows homology to parvulinlike prolyl isomerases. This domain is a well folded, stable protein and follows a simple two-state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm of E. coli as well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease-free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline-containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.Keywords: parvulin; Pin1; prolyl isomerase; SurA; protein maturation; periplasm; SecYEG Abbreviations: PpiD, periplasmic folding helper protein from Escherichia coli; PpiD*, parvulin-like domain of PpiD (residues 264-357); PPIase, peptidyl-prolyl cis/trans isomerase; CD, circular dichroism; T M , midpoint of a thermal unfolding transition; DH D , vań t Hoff enthalpy of denaturation at T M ; DG D , Gibbs free energy of denaturation; m, cooperativity value of a denaturant-induced equilibrium unfolding transition; Ds, time constant of a folding reaction; k u , microscopic rate constant and m u (¼ qlnk u /q[urea]), kinetic m-value of unfolding; k f , m f , microscopic rate constant and kinetic m-value of refolding; NOESY, nuclear Overhauser enhancement and exchange spectroscopy; HSQC, hetero single quantum coherence; hNOE, 15 N hetero nuclear NOE; HX, hydrogen exchange; NH, amide proton; RCM-T1, reduced and carboxymethylated form of the S54G/P55N double mutant of ribonuclease T 1 ; N2, N2 domain of the gene 3 protein of phage fd.Additional Supporting Information may be found in the online version of this article.

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“…This assay was validated for all three families of prolyl isomerases. 46 The prolyl isomerases SlyD [47][48][49] and cyclophi- could not accelerate this reaction [ Fig. 5(A)].…”

Section: Ppid* Does Not Catalyze Prolyl Isomerization In Peptides or mentioning

confidence: 99%

The prolyl isomerase domain of PpiD fromEscherichia colishows a parvulin fold but is devoid of catalytic activity

et al. 2009

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“…5,6 In a previous study, we successfully constructed an F36VIF hybrid by replacing the flap of F36V with an insertion-in-flap(IF) domain from sensitive-to-lysis D (SlyD) protein of Escherichia coli (E. coli). 7 The IF that was inserted was the 61-amino acid domain starting with AYG and ending with LKF that protrudes from a loop of the FKBP domain near the PPIase catalytic site, which is indicative of its hydrophobicity. The F36V mutant imparted a better model to fit ligands via this protruding structural part than FKBP12.…”

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confidence: 99%

Accelerated Fibril Formation of α-Synuclein by an IF-Inserted F36V Mutant

Shin¹,

Im²,

Lee

2013

Bulletin of the Korean Chemical Society

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“…SlyD contributes to both nickel accumulation and energy metabolism in this organism because it participates in the Ni(II) insertion step during [NiFe]-hydrogenase metallocenter assembly (4,5). NMR solution structures of E. coli SlyD revealed that the N-terminal region consists of two well-defined domains (6,7). The FKBP (FK-506 binding protein) domain has a similar structure as other members of the FKBP family of peptidyl-prolyl isomerases (PPIases) and catalyzes the otherwise slow isomerisation of proline peptide bonds during protein folding (8,9).…”

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confidence: 99%

“…In addition, the final 50 residues at the C-terminus of SlyD correspond to the metal-binding domain (MBD) and include 28 potential metal-binding amino acids (6 Cys, 15 His, 2 Glu, 5 Asp) ( Figure S1). This Cterminal domain remains unstructured according to NMR data and is variable between SlyD homologues (7,12). A vital role for the MBD of SlyD was established upon truncation of the protein in E. coli, which resulted in compromised hydrogenase production (13).…”

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confidence: 99%

Metal Selectivity of the Escherichia coli Nickel Metallochaperone, SlyD

et al. 2011

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SlyD is a Ni(II)-binding protein that contributes to nickel homeostasis in Escherichia coli. The Cterminal domain of SlyD contains a rich variety of metal-binding amino acids, suggesting broader metal-binding capabilities, and previous work demonstrated that the protein can coordinate several types of first row transition metals. However, the binding of SlyD to metals other than Ni(II) has not been previously characterized. To further our understanding of the in vitro metal-binding activity of SlyD and how it correlates with the in vivo function of this protein, the interactions between SlyD and the series of biologically relevant transition metals Mn(II), Fe(II), Co(II), Cu(I) and Zn(II) were examined by using a combination of optical spectroscopy and mass spectrometry. Tables S1-S3 containing a summary of metal concentrations used for metal toxicity studies, a list of primers used for qRT-PCR analysis and summary of Mn(II), Co(II) and Ni(II) stoichiometries of SlyD; Figure S2 shows representative spectra of a Ni(II) titrations analyzed via ESI-MS; Figures S3-S4 shows a graphical representation of the PAR competition assay used for determining the average K D (Zn(II)-SlyD) and a comparison of CD spectra for Ni(II) and Zn(II) bound SlyD. Figure S5 is a representative data set for a Cu(I) titration of SlyD analyzed via electronic absorption spectroscopy. Figure S6-S7 are competition titrations with Bca and Bcs used for determining copper stoichiometry and affinity, respectively. Figure S8-S10 are a graphical representation of Co(II) titrations analyzed via ESI-MS, competition titrations with Fura2 for determining average K D (Co(II)-SlyD) and titration of a cobalt saturated SlyD sample with Zn(II). Figure S11 is spectroscopy data obtained for titration of Ni(II) compared with a similar titration carried out in the presence of excess Fe(II). Figure S12 depicts representative growth curves of WT and ΔslyD strains conducted in minimal media supplemented with various amounts of metal. Figure S13 is relative mRNA levels measured for various metal transporters under aerobic conditions. Figure S14-S15 are relative mRNA levels measured for various metal transporters under anaerobic conditions. This material is available free of charge via the Internet at http://pubs.acs.org.

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NMR Solution Structure of SlyD from Escherichia coli: Spatial Separation of Prolyl Isomerase and Chaperone Function

Cited by 72 publications

References 44 publications

The prolyl isomerase domain of PpiD fromEscherichia colishows a parvulin fold but is devoid of catalytic activity

The prolyl isomerase domain of PpiD fromEscherichia colishows a parvulin fold but is devoid of catalytic activity

Accelerated Fibril Formation of α-Synuclein by an IF-Inserted F36V Mutant

Metal Selectivity of the Escherichia coli Nickel Metallochaperone, SlyD

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