Flexible Linker Region Research Articles

Design and probing of efflux functions of EGFP fused ABC membrane transporters in live cells using fluorescence spectroscopy

We have designed and constructed fusion genes of C-terminal (Ct) or N-terminal (Nt) bmrA with EGFP vectors and successfully expressed them in ΔBmrA (BmrA deletion strain of Bacillus subtilis), generating two new strains of B. subtilis (Ct-BmrA-EGFP and Nt-BmrA-EGFP). The fusion genes were characterized using gel electrophoresis and DNA sequencing. Their expression in live cells was determined by measuring the fluorescence of EGFP in single live cells using fluorescence microscopy and spectroscopy. The efflux function of the new strains was studied by measuring their accumulation kinetics of intracellular Hoechst dye molecules (a pump substrate) using fluorescence spectroscopy, which were compared with wild-type (WT-BmrA) and ΔBmrA strains. Both new strains show lower accumulation rates than ΔBmrA, and their efflux kinetics are inhibited by a pump inhibitor (orthovanadate). The results suggest that both strains extrude the dye molecules and the fusion proteins retain the efflux function of BmrA (ATP-binding cassette, ABC, transporter). Notably, Nt-BmrA-EGFP strain shows lower accumulation rates (higher efflux rates) than Ct-BmrA-EGFP. Modeled structures of the fusion proteins illustrate a highly flexible linker region connecting EGFP with BmrA, suggesting a minimal obstruction of EGFP to the BmrA. A closer distance of two C termini (~14 Å) than two N termini (47.9 Å) of the "closed" BmrA dimer depicts the larger steric effect of C-terminal fusion. This study also shows that glucose affects the fluorescence study of efflux function of BmrA, suggesting that efflux kinetics of ABC membrane transporters in live cells must be characterized in the absence of glucose.

Organization of PDZ Domains in Full-Length PSD-95

PDZ (PSD-95/Dlg/ZO-1) domains are small (∼90 amino acids) protein-interacting modules that canonically bind c-terminal recognition motifs. Multiple copies of PDZ domains within a single protein sequence are often required for the proper functioning of multidomain scaffold proteins. While the binding properties of isolated domains have been relatively well characterized, recent studies have demonstrated that interactions between PDZ domains are capable of modulating the binding affinities of individual domains. Interdomain association between PDZ domains may play a crucial role in the proper functioning of PDZ containing proteins but to date has been left largely uninvestigated. PSD-95 is the canonical member of the membrane associated guanylate kinase (MAGUK) family of PDZ containing proteins. Like all MAGUKs, PSD-95 is composed of three sequential PDZ domains followed by an SH3 domain and an enzymatically inactive guanylate kinase-like domain. The flexible linker regions between each PDZ domain and the apparent lack of a fixed domain organization have made it difficult to characterize these domains at the bulk ensemble level. Single-molecule FRET (smFRET) is a structural biology tool that is unaffected by the presence or absence of protein structures outside the regions of interest, and is capable of accurately measuring long range distances in dynamically fluctuating samples without the averaging effects inherent in ensemble measurements. smFRET measurements between multiple sites on each PDZ domain were used to observe the position and orientation of PDZ domains in both full-length PSD-95 as well as in truncated fragments. In combination with fluorescence correlation spectroscopy, isothermal titration calorimetry and molecular simulations, smFRET was used to determine the dynamic structure of PDZ domains in PSD-95 and to determine how this structure influences the binding modes for physiological ligands.

Molecular Recognition Mechanism of Calmodulin Examined by Perturbation-Response Scanning

Calmodulin (CaM) has a pivotal role as an intracellular Ca2+ receptor that is involved in calcium signaling pathways in eukaryotic cells [1,2]. Binding of Ca2+ and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner [1,3,4]. To design drugs that inhibit Ca2+-CaM formation, the molecular binding mechanism must be thoroughly understood.In this study, we use a new tool called perturbation-response scanning that is based on systematically exerting directed forces on the residues of the protein [5] and recording the changes in fluctuation profiles as the response. Different conformations of CaM are investigated to locate domains or key residues controlling ligand binding and release. We perform 200 ns long MD simulations on the apo form of CaM. The simulation is divided into chunks which resemble different conformations of the apo form. Using the cross-correlation matrices obtained from these chunks as the kernel in linear response, we determine the residues whose perturbation yields the experimentally determined displacement profiles of the apo and holo forms. We find that it is possible to induce the different conformational changes relevant to the binding of five different ligands, by perturbing varying ligand binding residues, and/or residues on the distant helices in the single apo-form. The findings thus give information on how the flexible linker region acts as a transducer of binding information to distant parts of the protein. This new tool enables us to reveal the essence of ligand recognition mechanisms by which CaM controls a wide variety of Ca2+ signaling processes.1. Ikura M. et.al., PNAS 103:1159-1164.2. Fallon J.L., et.al Structure 11:1303-1307.3. Vandonselaar M.,et.al., Struct.Biol. 1:795-801.4. Shepherd C.M., Vogel H.J., Biophys.J. 87:780-791.5. Atilgan C., Atilgan A.R., PloS Comput.Biol. 5:e1000544.

A flexible linker region in Fip1 is needed for efficient mRNA polyadenylation

Synthesis of the poly(A) tail of mRNA in Saccharomyces cerevisiae requires recruitment of the polymerase Pap1 to the 3' end of cleaved pre-mRNA. This is made possible by the tethering of Pap1 to the Cleavage/Polyadenylation Factor (CPF) by Fip1. We have recently reported that Fip1 is an unstructured protein in solution, and proposed that it might maintain this conformation as part of CPF, when bound to Pap1. However, the role that this feature of Fip1 plays in 3' end processing has not been investigated. We show here that Fip1 has a flexible linker in the middle of the protein, and that removal or replacement of the linker affects the efficiency of polyadenylation. However, the point of tethering is not crucial, as a fusion protein of Pap1 and Fip1 is fully functional in cells lacking genes encoding the essential individual proteins, and directly tethering Pap1 to RNA increases the rate of poly(A) addition. We also find that the linker region of Fip1 provides a platform for critical interactions with other parts of the processing machinery. Our results indicate that the Fip1 linker, through its flexibility and protein/protein interactions, allows Pap1 to reach the 3' end of the cleaved RNA and efficiently initiate poly(A) addition.

Post-translational processing of modular xylanases from Streptomyces is dependent on the carbohydrate-binding module

Xylanases are very often modular enzymes composed of one or more catalytic domains and carbohydrate-binding modules (CBMs) connected by a flexible linker region. Usually, when these proteins are processed they lose their carbohydrate-binding capacity. Here, the role of the linker regions and cellulose- or xylan-binding domains in the processing of Xys1L from Streptomyces halstedii JM8 and Xyl30L from Streptomyces avermitilis UAH30 was studied. Xys1 variants with different linker lengths were tested, these being unable to avoid protein processing. Moreover, several fusion proteins between the Xys1 and Xyl30 domains were obtained and their proteolytic stability was studied. We demonstrate that CBM processing takes place even in the complete absence of the linker sequence. We also show that the specific carbohydrate module determines this cleavage in the proteins studied.

Crystal Structures of a Populus tomentosa 4-Coumarate:CoA Ligase Shed Light on Its Enzymatic Mechanisms

4-Coumaric acid:CoA ligase (4CL) is the central enzyme of the plant-specific phenylpropanoid pathway. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters, the precursors of lignin and other important phenylpropanoids, in two-step reactions involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. In this study, we determined the crystal structures of Populus tomentosa 4CL1 in the unmodified (apo) form and in forms complexed with AMP and adenosine 5'-(3-(4-hydroxyphenyl)propyl)phosphate (APP), an intermediate analog, at 2.4, 2.5, and 1.9 Å resolution, respectively. 4CL1 consists of two globular domains connected by a flexible linker region. The larger N-domain contains a substrate binding pocket, while the C-domain contains catalytic residues. Upon binding of APP, the C-domain rotates 81° relative to the N-domain. The crystal structure of 4CL1-APP reveals its substrate binding pocket. We identified residues essential for catalytic activities (Lys-438, Gln-443, and Lys-523) and substrate binding (Tyr-236, Gly-306, Gly-331, Pro-337, and Val-338) based on their crystal structures and by means of mutagenesis and enzymatic activity studies. We also demonstrated that the size of the binding pocket is the most important factor in determining the substrate specificities of 4CL1. These findings shed light on the enzymatic mechanisms of 4CLs and provide a solid foundation for the bioengineering of these enzymes.

Actin Cross-link Assembly and Disassembly Mechanics for α-Actinin and Fascin

Self-assembly of complex structures is commonplace in biology but often poorly understood. In the case of the actin cytoskeleton, a great deal is known about the components that include higher order structures, such as lamellar meshes, filopodial bundles, and stress fibers. Each of these cytoskeletal structures contains actin filaments and cross-linking proteins, but the role of cross-linking proteins in the initial steps of structure formation has not been clearly elucidated. We employ an optical trapping assay to investigate the behaviors of two actin cross-linking proteins, fascin and alpha-actinin, during the first steps of structure assembly. Here, we show that these proteins have distinct binding characteristics that cause them to recognize and cross-link filaments that are arranged with specific geometries. alpha-Actinin is a promiscuous cross-linker, linking filaments over all angles. It retains this flexibility after cross-links are formed, maintaining a connection even when the link is rotated. Conversely, fascin is extremely selective, only cross-linking filaments in a parallel orientation. Surprisingly, bundles formed by either protein are extremely stable, persisting for over 0.5 h in a continuous wash. However, using fluorescence recovery after photobleaching and fluorescence decay experiments, we find that the stable fascin population can be rapidly competed away by free fascin. We present a simple avidity model for this cross-link dissociation behavior. Together, these results place constraints on how cytoskeletal structures assemble, organize, and disassemble in vivo.

Diminished Cooperativity: Comparing Linker Lengths in Synaptotagmin I C2A Domain

Exocytosis of neurotransmitters is triggered by the initial influx of Ca2+. Synaptotagmin I is known to bind Ca2+ and the phospholipid membrane to modulate this process. The exact mechanism for this information transduction, however, is not well known. Synaptotagmin I contains two binding domains, C2A and C2B, that are tethered to a neurotransmitter containing, lipid vesicle with a flexible linker region. The wild type C2A domain acts as a Ca2+ dependent trigger by binding the calcium ions in a cooperative manner. We seek to understand the role that the linker region has on the binding properties of the protein. To do this, a shortened construct (amino acids 141-267 verses amino acids 97-265 of the previously studied long construct) has been utilized as a probe to examine the effects of the truncated linker region. Ca2+ and phospholipid binding assays have been carried out and monitored via steady state fluorescence to make a thermodynamic comparison between the two constructs. Binding partition functions have been derived for this purpose and clearly show the diminished linkage relationship between the binding sites of the shortened construct.This material is based in part upon work supported by the National Science Foundation under CAREER-MCB 0747339

Focal localization of MukBEF condensin on the chromosome requires the flexible linker region of MukF

Condensin complexes are the key mediators of chromosome condensation. The MukB-MukE-MukF complex is a bacterial condensin, in which the MukB subunit forms a V-shaped dimeric structure with two ATPase head domains. MukE and MukF together form a tight complex, which binds to the MukB head via the C-terminal winged-helix domain (C-WHD) of MukF. One of the two bound C-WHDs of MukF is forced to detach from two ATP-bound, engaged MukB heads, and this detachment reaction depends on the MukF flexible linker preceding the C-WHD. Whereas MukB is known to focally localize at particular positions in cells by an unknown mechanism, mukE- or mukF-null mutation causes MukB to become dispersed in cells. Here, we report that mutations in MukF causing a defect in the detachment reaction interfere with the focal localization of MukB, and that the dispersed distribution of MukB in cells correlates directly with defects in cell growth and division. The data strongly suggest that the MukB-MukE-MukF condensin forms huge clusters through the ATP-dependent detachment reaction, and this cluster formation is critical for chromosome condensation by this machinery. We also show that the MukF flexible linker is involved in the dimerization and ATPase activity of the MukB head.

Structural characterization of a novel Ca2+-binding protein from Entamoeba histolytica: structural basis for the observed functional differences with its isoform

A novel Ca(2+)-binding protein (EhCaBP2) was identified from the protozoan parasite Entamoeba histolytica. EhCaBP2 has 79% sequence identity with calcium-binding protein EhCaBP1. The 3D structure of EhCaBP2 was determined using multidimensional nuclear magnetic resonance spectroscopic techniques. The study reveals that the protein consists of two globular domains connected by a short flexible linker region of four residues. On comparison of the 3D structure and dynamics of EhCaBP2 with those of EhCaBP1, it is found that they vary significantly in their N-terminal domains and interdomain linker. Immunofluorescence localization experiments revealed that EhCaBP1 and EhCaBP2 may not carry out similar functions, as their cellular distribution patterns are not the same. The functional differences between the two isoforms are explained on the basis of results obtained from the structural studies. The structural variation in the interdomain linker region and the formation of functionally important hydrophobic clefts in different regions of EhCaBP1 and EhCaBP2 provide interesting insights into the differences in the functionality of these two isoforms.

A Catalytic Role of Heparin within the Extracellular Matrix

We investigated the mechanism by which heparin enhances the binding of vascular endothelial growth factor (VEGF) to the extracellular matrix protein fibronectin. In contrast to other systems, where heparin acts as a protein scaffold, we found that heparin functions catalytically to modulate VEGF binding site availability on fibronectin. By measuring the binding of VEGF and heparin to surface-immobilized fibronectin, we show that substoichiometric amounts of heparin exposed cryptic VEGF binding sites within fibronectin that remain available after heparin removal. Measurement of association and dissociation kinetics for heparin binding to fibronectin indicated that the interaction is rapid and transient. We localized the heparin-responsive element to the C-terminal 40-kDa Hep2 domain of fibronectin. A mathematical model of this catalytic process was constructed that supports a mechanism whereby the heparin-induced conformational change in fibronectin is accompanied by release of heparin. Experiments with endothelial extracellular matrix suggest that this process may also occur within biological matrices. These results indicate a novel mechanism whereby heparin catalyzes the conversion of fibronectin to an open conformation by transiently interacting with fibronectin and progressively hopping from molecule to molecule. Catalytic activation of the extracellular matrix might be an important mechanism for heparin to regulate function during normal and disease states.

Chaperone-Assisted Crystallography with DARPins

The structure of proteins that are difficult to crystallize can often be solved by forming a noncovalent complex with a helper protein--a crystallization "chaperone." Although several such applications have been described to date, their handling usually is still very laborious. A valuable addition to the present repertoire of binding proteins is the recently developed designed ankyrin repeat protein (DARPin) technology. DARPins are built based on the natural ankyrin repeat protein fold with randomized surface residue positions allowing specific binding to virtually any target protein. The broad potential of these binding proteins for X-ray crystallography is illustrated by five cocrystal structures that have been determined recently comprising target proteins from distinct families, namely a sugar binding protein, two kinases, a caspase, and a membrane protein. This article reviews the opportunities of this technology for structural biology and the structural aspects of the DARPin-protein complexes.

Munc18a Scaffolds SNARE Assembly to Promote Membrane Fusion

Munc18a is an SM protein required for SNARE-mediated fusion. The molecular details of how Munc18a acts to enhance neurosecretion have remained elusive. Here, we use in vitro fusion assays to characterize how specific interactions between Munc18a and the neuronal SNAREs enhance the rate and extent of fusion. We show that Munc18a interacts directly and functionally with the preassembled t-SNARE complex. Analysis of Munc18a point mutations indicates that Munc18a interacts with helix C of the Syntaxin1a NRD in the t-SNARE complex. Replacement of the t-SNARE SNAP25b with yeast Sec9c had little effect, suggesting that Munc18a has minimal contact with SNAP25b within the t-SNARE complex. A chimeric Syntaxin built of the Syntaxin1a NRD and the H3 domain of yeast Sso1p and paired with Sec9c eliminated stimulation of fusion, suggesting that Munc18a/Syntaxin1a H3 domain contacts are important. Additionally, a Syntaxin1A mutant lacking a flexible linker region that allows NRD movement abolished stimulation of fusion. These experiments suggest that Munc18a binds to the Syntaxin1a NRD and H3 domain within the assembled t-SNARE complex, positioning them for productive VAMP2 binding. In this capacity, Munc18a serves as a platform for trans-SNARE complex assembly that facilitates efficient SNARE-mediated membrane fusion.

The Tyrosine Phosphorylation of Munc18c Induces a Switch in Binding Specificity from Syntaxin 4 to Doc2β

Glucose-stimulated insulin secretion is mediated by syntaxin 4-based SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes and the Sec1/Munc18 protein Munc18c. Our laboratory recently reported that Munc18c-syntaxin 4 complexes are further regulated by the competitive binding of the double C2 domain protein Doc2beta to Munc18c, although the underlying mechanism for this is unknown. Because the Doc2beta binding region of Munc18c contained residue Tyr-219 and this residue becomes phosphorylated in response to glucose stimulation, we hypothesized that the mechanism would involve Munc18c phosphorylation. Coimmunoprecipitation analyses using detergent lysates prepared from pervanadate-treated MIN6 beta cells revealed that the tyrosine phosphorylation of Munc18c corresponded to a 60% decrease in Munc18c-syntaxin 4 association with a coordinate 2-fold increase in Munc18c-Doc2beta binding. In vitro binding assays identified syntaxin 4 residues 118-194 as sufficient to confer its interaction with Munc18c; residues 118-194 contain the Hc alpha-helix and flexible linker region controlling transition of syntaxins between closed and open conformations. When overexpressed in MIN6 cells, this Hc-linker region functioned as a competitive inhibitor of endogenous syntaxin 4-Munc18c binding, increased syntaxin 4 binding to VAMP2, and significantly enhanced glucose-stimulated secretion. Molecular modeling of these new interactions yielded the predictions 1) that Tyr-219 of Munc18c remains buried under basal conditions in a conformation that is favorable for interaction with "closed" syntaxin 4 and 2) that stimulation leads to changes in syntaxin 4 contacts to facilitate exposure of Munc18c Tyr-219 for phosphorylation and Doc2beta binding.

The Allosteric Role of the Ca2+ Switch in Adhesion and Elasticity of C-Cadherin

Modular proteins such as titin, fibronectin, and cadherin are ubiquitous components of living cells. Often involved in signaling and mechanical processes, their architecture is characterized by domains containing a variable number of heterogeneous “repeats” arranged in series, with either flexible or rigid linker regions that determine their elasticity. Cadherin repeats arranged in series are unique in that linker regions also feature calcium-binding motifs. While it is well known that the extracellular repeats of cadherin proteins mediate cell-cell adhesion in a calcium-dependent manner, the molecular mechanisms behind the influence of calcium in adhesion dynamics and cadherin's mechanical response are not well understood. Here we show, using molecular dynamics simulations, how calcium ions control the structural integrity of cadherin's linker regions, thereby affecting cadherin's equilibrium dynamics, the availability of key residues involved in cell-cell adhesion, and cadherin's mechanical response. The all-atom, multi-nanosecond molecular dynamics simulations involved the entire C-cadherin extracellular domain solvated in water (a 345,000 atom system). Equilibrium simulations show that the extracellular domain maintains its crystal conformation (elongated and slightly curved) when calcium ions are present. In the absence of calcium ions, however, it assumes a disordered conformation. The conserved residue Trp2, which is thought to insert itself into a hydrophobic pocket of another cadherin molecule (thereby providing the basis for cell-cell adhesion), switches conformation from exposed to intermittently buried upon removal of calcium ions. Furthermore, the overall mechanical response of C-cadherin's extracellular domain is characterized at low force by changes in shape (tertiary structure elasticity), and at high force by unraveling of secondary structure elements (secondary structure elasticity). This mechanical response is modulated by calcium ions at both low and high force, switching from a stiff, rod-like to a soft, spring-like behavior upon removal of ions. The simulations provide an unprecedented molecular view of calcium-mediated allostery in cadherins, also illustrating the general principles of linker-mediated elasticity of modular proteins relevant not only for cell-cell adhesion and sound transduction, but also muscle elasticity.

Annexin A6-induced Inhibition of Cytoplasmic Phospholipase A2 Is Linked to Caveolin-1 Export from the Golgi

The molecular mechanisms regulating the exit of caveolin from the Golgi complex are not fully understood. Cholesterol and sphingolipid availability affects Golgi vesiculation events and involves the activity of cytoplasmic phospholipase A(2) (cPLA(2)). We recently demonstrated that high expression levels of annexin A6 (AnxA6) perturb the intracellular distribution of cellular cholesterol, thereby inhibiting caveolin export from the Golgi complex. In the present study we show that in Chinese hamster ovary cells overexpressing AnxA6, sequestration of cholesterol in late endosomes, leading to reduced amounts of cholesterol in the Golgi, inhibits cPLA(2) activity and its association with the Golgi complex. This correlates with the blockage of caveolin export from the Golgi in cells treated with methyl arachidonyl fluorophosphonate, a Ca(2+)-dependent cPLA(2) inhibitor. AnxA6-mediated down-regulation of cPLA(2) activity was overcome upon the addition of exogenous cholesterol or transfection with small interfering RNA targeting AnxA6. These findings indicate that AnxA6 interferes with caveolin transport through the inhibition of cPLA(2).

The binding and activation of Nitric Oxide Synthase by modified central linker and “phosphomimetic” Calmodulin proteins

Calmodulin (CaM) is a ubiquitous calcium‐binding protein that is known to interact and regulate hundreds of intercellular functional proteins. The promiscuity of CaM is partially due to its highly flexible central linker region that separates its two terminal domains which interact with its target protein. Modification of the central linker region of CaM can result in changes in the proximity of the two terminal domains, their relative orientation, binding affinity and activation of the CaM target proteins. The present study was designed to investigate the role of the central linker of CaM by introducing select mutations, including phosphomimetic residues, into the CaM central linker region. The effects of these modifications on the binding and activation of the three mammalian nitric oxide synthase (NOS) isozymes have been investigated using biophysical techniques including circular dichroism, FTIR and gel shift mobility assays. Assays have been performed to assess the effect that modified CaM linker residues have on NOS enzyme activation and electron transfer. This research is supported by NSERC (J.G.G.)

Molecular Dynamics Simulations of Two Tandem Octarepeats from the Mammalian Prion Protein: Fully Cu 2+-bound and Metal-Free Forms

Molecular dynamics simulations have been conducted on a model fragment (Ac-PHGGGWGQPHGGGW-NH 2) of the prion protein octarepeat domain, both in the Cu 2+-bound and metal-free forms. The copper-bound models are based on the consensus structure of the core Cu 2+-binding site of an individual octarepeat, relevant to the fully Cu 2+-occupied prion protein octarepeat region. The model peptides contain Cu 2+ bound through a His imidazole ring and two deprotonated amide N-atoms in the peptide backbone supplied by the following two Gly residues. Both the copper-bound and metal-free models have been simulated with the OPLS all-atom force field with the GROMACS molecular dynamics package. These simulations, with two tandem copper-binding sites, represent the minimum model necessary to observe potential structuring between the copper-binding sites in the octarepeat region. The GWGQ residues constitute a flexible linker region that predominantly adopts a turn, serving to bring adjacent His residues into close proximity. The consequent formation of stable structures demonstrates that the copper-bound octarepeat region allows the copper-coordinating sites to come into van der Waals contact, packing into particular orientations to further stabilize the bend in the GWGQ linker region.

The linker region plays a key role in the adaptation to cold of the cellulase from an Antarctic bacterium

The psychrophilic cellulase, Cel5G, from the Antarctic bacterium Pseudoalteromonas haloplanktis is composed of a catalytic module (CM) joined to a carbohydrate-binding module (CBM) by an unusually long, extended and flexible linker region (LR) containing three loops closed by three disulfide bridges. To evaluate the possible role of this region in cold adaptation, the LR was sequentially shortened by protein engineering, successively deleting one and two loops of this module, whereas the last disulfide bridge was also suppressed by replacing the last two cysteine residue by two alanine residues. The kinetic and thermodynamic properties of the mutants were compared with those of the full-length enzyme, and also with those of the cold-adapted CM alone and with those of the homologous mesophilic enzyme, Cel5A, from Erwinia chrysanthemi. The thermostability of the mutated enzymes as well as their relative flexibility were evaluated by differential scanning calorimetry and fluorescence quenching respectively. The topology of the structure of the shortest mutant was determined by SAXS (small-angle X-ray scattering). The data indicate that the sequential shortening of the LR induces a regular decrease of the specific activity towards macromolecular substrates, reduces the relative flexibility and concomitantly increases the thermostability of the shortened enzymes. This demonstrates that the long LR of the full-length enzyme favours the catalytic efficiency at low and moderate temperatures by rendering the structure not only less compact, but also less stable, and plays a crucial role in the adaptation to cold of this cellulolytic enzyme.

Structural Organization of Essential Iron-Sulfur Clusters in the Evolutionarily Highly Conserved ATP-binding Cassette Protein ABCE1

The ABC protein ABCE1, formerly named RNase L inhibitor RLI1, is one of the most conserved proteins in evolution and is expressed in all organisms except eubacteria. Because of its fundamental role in translation initiation and/or ribosome biosynthesis, ABCE1 is essential for life. Its molecular mechanism has, however, not been elucidated. In addition to two ABC ATPase domains, ABCE1 contains a unique N-terminal region with eight conserved cysteines, predicted to coordinate iron-sulfur clusters. Here we present detailed information on the type and on the structural organization of the Fe-S clusters in ABCE1. Based on biophysical, biochemical, and yeast genetic analyses, ABCE1 harbors two essential diamagnetic [4Fe-4S](2+) clusters with different electronic environments, one ferredoxin-like (CPX(n)CX(2)CX(2)C; Cys at positions 4-7) and one unique ABCE1-type cluster (CXPX(2)CX(3)CX(n)CP; Cys at positions 1, 2, 3, and 8). Strikingly, only seven of the eight conserved cysteines coordinating the Fe-S clusters are essential for cell viability. Mutagenesis of the cysteine at position 6 yielded a functional ABCE1 with the ferredoxin-like Fe-S cluster in a paramagnetic [3Fe-4S](+) state. Notably, a lethal mutation of the cysteine at position 4 can be rescued by ligand swapping with an adjacent, extra cysteine conserved among all eukaryotes.