Flexible C-terminal Extension Research Articles

Influenza virus Matrix Protein M1 preserves its conformation with pH, changing multimerization state at the priming stage due to electrostatics

Influenza A virus matrix protein M1 plays an essential role in the virus lifecycle, but its functional and structural properties are not entirely defined. Here we employed small-angle X-ray scattering, atomic force microscopy and zeta-potential measurements to characterize the overall structure and association behavior of the full-length M1 at different pH conditions. We demonstrate that the protein consists of a globular N-terminal domain and a flexible C-terminal extension. The globular N-terminal domain of M1 monomers appears preserved in the range of pH from 4.0 to 6.8, while the C-terminal domain remains flexible and the tendency to form multimers changes dramatically. We found that the protein multimerization process is reversible, whereby the binding between M1 molecules starts to break around pH 6. A predicted electrostatic model of M1 self-assembly at different pH revealed a good agreement with zeta-potential measurements, allowing one to assess the role of M1 domains in M1-M1 and M1-lipid interactions. Together with the protein sequence analysis, these results provide insights into the mechanism of M1 scaffold formation and the major role of the flexible and disordered C-terminal domain in this process.

Crystal Structure of the LysY·LysW Complex from Thermus thermophilus

Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of α-aminoadipate (AAA). The resulting LysW-γ-AAA is phosphorylated by LysZ to form LysW-γ-AAA phosphate, which is subsequently reduced to LysW-γ-aminoadipic semialdehyde (LysW-γ-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-γ-AASA and TtLysW-γ-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix α9 and the β11-α10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ·TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.

Structures of the CDK12/CycK complex with AMP-PNP reveal a flexible C-terminal kinase extension important for ATP binding.

Cyclin-dependent kinase 12 (CDK12) promotes transcriptional elongation by phosphorylation of the RNA polymerase II C-terminal domain (CTD). Structure-function studies show that this activity is dependent on a C-terminal kinase extension, as well as the binding of cyclin K (CycK). To better define these interactions we determined the crystal structure of the human CDK12/CycK complex with and without the kinase extension in the presence of AMP-PNP. The structures revealed novel features for a CDK, including a large β4-β5 loop insertion that contributes to the N-lobe interaction with the cyclin. We also observed two different conformations of the C-terminal kinase extension that effectively open and close the ATP pocket. Most notably, bound AMP-PNP was only observed when trapped in the closed state. Truncation of this C-terminal structure also diminished AMP-PNP binding, as well as the catalytic activity of the CDK12/CycK complex. Further kinetic measurements showed that the full length CDK12/CycK complex was significantly more active than the two crystallised constructs suggesting a critical role for additional domains. Overall, these results demonstrate the intrinsic flexibility of the C-terminal extension in CDK12 and highlight its importance for both ATP binding and kinase activity.

The Heme Chaperone ApoCcmE Forms a Ternary Complex with CcmI and Apocytochrome c

Cytochrome c maturation (Ccm) is a post-translational process that occurs after translocation of apocytochromes c to the positive (p) side of energy-transducing membranes. Ccm is responsible for the formation of covalent bonds between the thiol groups of two cysteines residues at the heme-binding sites of the apocytochromes and the vinyl groups of heme b (protoporphyrin IX-Fe). Among the proteins (CcmABCDEFGHI and CcdA) required for this process, CcmABCD are involved in loading heme b to apoCcmE. The holoCcmE thus formed provides heme b to the apocytochromes. Catalysis of the thioether bonds between the apocytochromes c and heme b is mediated by the heme ligation core complex, which in Rhodobacter capsulatus contains at least the CcmF, CcmH, and CcmI components. In this work we show that the heme chaperone apoCcmE binds to the apocytochrome c and the apocytochrome c chaperone CcmI to yield stable binary and ternary complexes in the absence of heme in vitro. We found that during these protein-protein interactions, apoCcmE favors the presence of a disulfide bond at the apocytochrome c heme-binding site. We also establish using detergent-dispersed membranes that apoCcmE interacts directly with CcmI and CcmH of the heme ligation core complex CcmFHI. Implications of these findings are discussed with respect to heme transfer from CcmE to the apocytochromes c during heme ligation assisted by the core complex CcmFHI.

NMR spectroscopy of 14-3-3ζ reveals a flexible C-terminal extension: differentiation of the chaperone and phosphoserine-binding activities of 14-3-3ζ

Intracellular 14-3-3 proteins bind to many proteins, via a specific phosphoserine motif, regulating diverse cellular tasks including cell signalling and disease progression. The 14-3-3ζ isoform is a molecular chaperone, preventing the stress-induced aggregation of target proteins in a manner comparable with that of the unrelated sHsps (small heat-shock proteins). 1H-NMR spectroscopy revealed the presence of a flexible and unstructured C-terminal extension, 12 amino acids in length, which protrudes from the domain core of 14-3-3ζ and is similar in structure and length to the C-terminal extension of mammalian sHsps. The extension stabilizes 14-3-3ζ, but has no direct role in chaperone action. Lys(49) is an important functional residue within the ligand-binding groove of 14-3-3ζ with K49E 14-3-3ζ exhibiting markedly reduced binding to phosphorylated and non-phosphorylated ligands. The R18 peptide binds to the binding groove of 14-3-3ζ with high affinity and also reduces the interaction of 14-3-3ζ ligands. However, neither the K49E mutation nor the presence of the R18 peptide affected the chaperone activity of 14-3-3ζ, implying that the C-terminal extension and binding groove of 14-3-3ζ do not mediate interaction with target proteins during chaperone action. Other region(s) in 14-3-3ζ are most likely to be involved, i.e. the protein's chaperone and phosphoserine-binding activities are functionally and structurally separated.

Site-Directed Mutations in the C-Terminal Extension of Human αB-Crystallin Affect Chaperone Function and Block Amyloid Fibril Formation

BackgroundAlzheimer's, Parkinson's and Creutzfeldt-Jakob disease are associated with inappropriate protein deposition and ordered amyloid fibril assembly. Molecular chaperones, including αB-crystallin, play a role in the prevention of protein deposition.Methodology/Principal FindingsA series of site-directed mutants of the human molecular chaperone, αB-crystallin, were constructed which focused on the flexible C-terminal extension of the protein. We investigated the structural role of this region as well as its role in the chaperone function of αB-crystallin under different types of protein aggregation, i.e. disordered amorphous aggregation and ordered amyloid fibril assembly. It was found that mutation of lysine and glutamic acid residues in the C-terminal extension of αB-crystallin resulted in proteins that had improved chaperone activity against amyloid fibril forming target proteins compared to the wild-type protein.Conclusions/SignificanceTogether, our results highlight the important role of the C-terminal region of αB-crystallin in regulating its secondary, tertiary and quaternary structure and conferring thermostability to the protein. The capacity to genetically modify αB-crystallin for improved ability to block amyloid fibril formation provides a platform for the future use of such engineered molecules in treatment of diseases caused by amyloid fibril formation.

The small heat shock proteins and their role in human disease

Small heat shock proteins (sHSPs) function as molecular chaperones, preventing stress induced aggregation of partially denatured proteins and promoting their return to native conformations when favorable conditions pertain. Sequence similarity between sHSPs resides predominately in an internal stretch of residues termed the alpha-crystallin domain, a region usually flanked by two extensions. The poorly conserved N-terminal extension influences oligomer construction and chaperone activity, whereas the flexible C-terminal extension stabilizes quaternary structure and enhances protein/substrate complex solubility. sHSP polypeptides assemble into dynamic oligomers which undergo subunit exchange and they bind a wide range of cellular substrates. As molecular chaperones, the sHSPs protect protein structure and activity, thereby preventing disease, but they may contribute to cell malfunction when perturbed. For example, sHSPs prevent cataract in the mammalian lens and guard against ischemic and reperfusion injury due to heart attack and stroke. On the other hand, mutated sHSPs are implicated in diseases such as desmin-related myopathy and they have an uncertain relationship to neurological disorders including Parkinson's and Alzheimer's disease. This review explores the involvement of sHSPs in disease and their potential for therapeutic intervention.

Pseudo-atomic models of swollen CCMV from cryo-electron microscopy data

The capsid of cowpea chlorotic mottle virus (CCMV) can reversibly switch between two forms that are contingent on the charge of acidic residues that are clustered at the quasi-threefold axes of the T=3 icosahedral particle. The quaternary structure conformations are dependent on divalent metal ions and pH and were previously analyzed by crystallography in the native, compact form, and by cryo-electron microscopy in the compact and swollen forms ( Speir et al., 1995). In this report we use the atomic models of the three structurally unique viral subunits determined by crystallography for a detailed interpretation of the 28-Å-resolution electron density of the swollen form and the production of a pseudo-atomic model of this particle. The model of the quaternary structure conforms with high fidelity to conventional geometric constraints, quasi-equivalence, intersubunit association energies, and the electron density. It was derived by conserving the pentamers and hexamers of subunits whose associated electron densities are strikingly similar in the two forms of the particles. Treating these as rigid units in the modeling implies that the particle flexibility is accommodated primarily by changes in dimer interactions, an observation that is consistent with the flexible C-terminal polypeptide extensions that stabilize this contact in the crystal structure. Because the hexamers and pentamers were incrementally translated and rotated in a screw motion, with energy minimization at each of 28 steps, a path for the expansion is also implied.

A small-angle X-ray solution scattering study of bovine alpha-crystallin.

The native high molecular mass form of alpha-crystallin, the most important soluble protein in the eye lens, and its low molecular mass form obtained at 37 degrees C in dilute solutions were investigated by synchrotron radiation small-angle X-ray scattering. The alpha-crystallin solutions are polydisperse and good fits to the experimental data can be obtained using distributions of spheres with radii varying between about 5 and 10 nm. In spite of the polydispersity, two different ab initio methods were used to retrieve low resolution shapes from the scattering data. These shapes correspond to the z-average structure of the oligomers. In the absence of any symmetry constraints, the scattering curves of the two forms of alpha-crystallin yield bean-like shapes. The shape corresponding to the low molecular mass form has about 20% less mass at the periphery. Imposing tetrahedral symmetry on the average structures worsens the fit to the experimental data. We emphasized the apparent contradiction between hydrodynamic and molecular properties of alpha-crystallin. An explanation was put forward based on the presence of solvent-exposed flexible C-terminal extensions. We present two bead models ('hollow globule with tentacles' and 'bean with tentacles') based on NMR and cryo-electron microscopy studies and discuss how well they correspond with our data from X-ray scattering, light scattering and analytical ultracentrifugation.

Mouse Hsp25, a small shock protein. The role of its C-terminal extension in oligomerization and chaperone action.

Under conditions of cellular stress, small heat shock proteins (sHsps), e.g. Hsp25, stabilize unfolding proteins and prevent their precipitation from solution. 1H NMR spectroscopy has shown that mammalian sHsps possess short, polar and highly flexible C-terminal extensions. A mutant of mouse Hsp25 without this extension has been constructed. CD spectroscopy reveals some differences in secondary and tertiary structure between this mutant and the wild-type protein but analytical ultracentrifugation and electron microscopy show that the proteins have very similar oligomeric masses and quaternary structures. The mutant shows chaperone ability comparable to that of wild-type Hsp25 in a thermal aggregation assay using citrate synthase, but does not stabilize alpha-lactalbumin against precipitation following reduction with dithiothreitol. The accessible hydrophobic surface of the mutant protein is less than that of the wild-type protein and the mutant is also less stable at elevated temperature. 1H NMR spectroscopy reveals that deletion of the C-terminal extension of Hsp25 leads to induction of extra C-terminal flexibility in the molecule. Monitoring complex formation between Hsp25 and dithiothreitol-reduced alpha-lactalbumin by 1H NMR spectroscopy indicates that the C-terminal extension of Hsp25 retains its flexibility during this interaction. Overall, these data suggest that a highly flexible C-terminal extension in mammalian sHsps is required for full chaperone activity.

Probing the structure and interactions of crystallin proteins by NMR spectroscopy.

The lens is composed primarily of proteins, the crystallins, at high concentration whose structure and interactions are responsible for lens transparency. As there is no protein turnover in the majority of the lens, crystallin proteins have to be very stable and long-lived proteins. There are three types of crystallin proteins: alpha, beta and gamma, and they all are composed of a variety of subunits. In addition, extensive post-translational modification is undergone by many of the subunits. Determining the structural features and the preferential interactions and associations undergone by the crystallin proteins in the lens is a large and complex experimental undertaking. Some progress has been made in this area by X-ray crystallographic determination of structures for representative examples of the beta- and gamma-crystallins [Slingsby, C., Norledge, B., Simpson, A., Bateman, O. A., Wright, G., Driessen H. P. C., Lindley, P. F., Moss, D. S. and Bax, B. (1997) X-ray diffraction and structure of crystallins. Prog. Ret. Eye Res. 16, 3-29]. In this article, a summary is given of nuclear magnetic resonance (NMR) methods to determine information about these aspects of crystallin proteins. It is shown that despite their relatively large size, all crystallins give rise to well-resolved NMR spectra which arise from flexible terminal extensions that extend from the domain core of the proteins. By examining NMR spectra of mixtures of different crystallin subunits, it is possible to determine the role of these extensions in crystallin-crystallin interactions. For example, the flexible C-terminal extensions in the two alpha-crystallin subunits are not involved in interacting with the other crystallins but are crucially important in the chaperone action of alpha-crystallin. In this action, alpha-crystallin stabilises other proteins under conditions of stress, e.g. heat. In the lens, this ability probably has important consequences in preventing the precipitation of crystallin proteins with age and thereby contributing to cataract formation. The C-terminal extensions in alpha-crystallin act as solubilising agents for the protein and the high-molecular-weight complex that forms upon chaperone action with a precipitating "substrate" protein. Similar behaviour is observed for a variety of small heat-shock proteins, to which alpha-crystallin is related. NMR studies are also consistent with a two-domain structure for alpha-crystallin. No crystal structure is available for crystallin. Using the NMR data, a model for the quaternary structure of alpha-crystallin is proposed which comprises an annular arrangement for the subunits with a large central cavity.

Alpha-crystallin as a molecular chaperone.

The role of alpha-crystallin as a molecular chaperone may explain how the lens stays transparent for so long. Alpha-crystallin prevents the aggregation of other lens crystallins and proteins that have become unfolded by "trapping" the protein in a high molecular weight complex. It also protects enzyme activities. The substrate protein may interact while in a molten globule state. Alpha-crystallin predominantly binds to proteins very early in the denaturation pathways. The amphiphilic nature of alpha-crystallin, a polar C-terminal-region and a hydrophobic N-terminal-region are all essential for chaperone function. The flexible C-terminal extension maintains solubility and can bind to opposing charged residues of unfolding proteins. Hydrophobic regions in the N-terminal region then hold the unfolded protein. Specific areas important for chaperone binding and function have been identified throughout the N-terminal-region, connecting peptide and C-terminal extension. After a substantial amount of chemical data and models, cryo-EM images of alpha-crystallin have confirmed a variable 3D surface with a hollow interior. Alpha-crystallin taken from the lens nucleus shows an age-dependent decrease in chaperone function. High molecular weight aggregates and alpha-crystallin found within the nucleus from clear and cataract lenses have reduced chaperone function. Post-translational modifications, known to occur during ageing, such as glycation, carbamylation, oxidation, phosphorylation and truncation cause a decrease in chaperone function. Alpha-crystallin is expressed outside the lens. AlphaB-crystallin can be induced by heat shock in many tissues where it is translocated from cytoplasm to nucleus. Increased expression of alphaB-crystallin has been seen in many pathological states. Conformational disorders, including cataract may have a common aetiology and potentially a common therapy.

NMR spectroscopy of α-crystallin. Insights into the structure, interactions and chaperone action of small heat-shock proteins

The subunit molecular mass of α-crystallin, like many small heat-shock proteins (sHsps), is around 20 kDa although the protein exists as a large aggregate of average mass around 800 kDa. Despite this large size, a well-resolved 1H NMR spectrum is observed for α-crystallin which arises from short, polar, highly-flexible and solvent-exposed C-terminal extensions in each of the subunits, αA- and αB-crystallin. These extensions are not involved in interactions with other proteins (e.g. β- and γ-crystallins) under non-chaperone conditions. As determined by NMR studies on mutants of αA-crystallin with alterations in its C-terminal extension, the extensions have an important role in acting as solubilising agents for the relatively-hydrophobic α-crystallin molecule and the high-molecular-weight (HMW) complex that forms during the chaperone action. The related sHsp, Hsp25, also exhibits a flexible C-terminal extension. Under chaperone conditions, and in the HMW complex isolated from old lenses, the C-terminal extension of the αA-crystallin subunit maintains its flexibility whereas the αB-crystallin subunit loses, at least partially, its flexibility, implying that it is involved in interaction with the ‘substrate’ protein. The conformation of ‘substrate’ proteins when they interact with α-crystallin has been probed by 1H NMR spectroscopy and it is concluded that α-crystallin interacts with ‘substrate’ proteins that are in a disordered molten globule state, but only when this state is on its way to large-scale aggregation and precipitation. By monitoring the 1H and 31P NMR spectra of α-crystallin in the presence of increasing concentations of urea, it is proposed that α-crystallin adopts a two-domain structure with the larger C-terminal domain unfolding first in the presence of denaturant. All these data have been combined into a model for the quaternary structure of α-crystallin. The model has two layers each of approximately 40 subunits arranged in an annulus or toroid. A large central cavity is present whose entrance is ringed by the flexible C-terminal extensions. A large hydrophobic region in the aggregate is exposed to solution and is available for interaction with ‘substrate’ proteins during the chaperone action.

A spectroscopic study of glycated bovine α-crystallin: investigation of flexibility of the C-terminal extension, chaperone activity and evidence for diglycation

The effect of glycating the C-terminal extensions of α-crystallin on their flexibility was investigated. In the course of the study the reaction sites were identified and double glycation of single lysine residues was found. α-Crystallin was incubated until approximately one mole of the sugar had reacted per subunit of the crystallin. The reaction sites were investigated by mass spectrometry and 1 H NMR spectroscopy, and were found to be principally in the short and flexible C-terminal extensions. The chaperone ability of α-crystallin was unaffected by this limited glycation. There was little effect on the flexibility of the C-terminal extensions. This result supports the view that the flexibility of the C-terminal extensions of α-crystallin is important for chaperone activity. As α-crystallin consists of a mixture of unmodified and phosphorylated subunits, a detailed investigation was undertaken of the reaction of galactose with peptides comprising the C-terminal extensions of αA- and αB-crystallin. The αA peptide was incubated with galactose until 0.79 mole of sugar was bound per mole of peptide and the αB peptide reacted until 2.2 moles of galactose had been incorporated. The purified glycated peptides were examined by NMR and mass spectrometry to identify glycation site(s), and the effect of glycation on the conformation of the peptides. For both peptides, it was found that extensive glycation of the constituent lysine residues occurred. The addition of two galactose molecules to some lysine residues of the peptides was also noted. This diglycation was confirmed in control experiments with N-acetyl-lysine.

1H NMR spectroscopy reveals that mouse Hsp25 has a flexible C-terminal extension of 18 amino acids

The small heat-shock proteins (Hsps) exist as large aggregates and function by interacting and stabilising non-native proteins in a chaperone-like manner. Two-dimensional 1H NMR spectroscopy of mouse Hsp25 reveals that the last 18 amino acids have great flexibility with motion that is essentially independent of the domain core of the protein. The lens protein, α-crystallin, is homologous to Hsp25 and its two subunits also have flexible C-terminal extensions. The flexible region in Hsp25 encompasses exactly that expected from sequence comparison with α-crystallin implying that both proteins have similar structures and that the C-terminal extensions could be of functional importance for both proteins.

Supramolecular Order within the Lens: 1H NMR Spectroscopic Evidence for Specific Crystallin-Crystallin Interactions

α-, β- and γ-crystallins from bovine lens contain flexible terminal extensions which are readily observed by NMR spectroscopy. By monitoring these resonances, NMR spectroscopy therefore offers a means of examining specific protein-protein interactions in crystallin mixtures. In this paper, a 1H NMR spectroscopic study of bovine lens nuclear and cortical homogenates and various crystallin mixtures is presented. In both homogenates, resonances from the flexible C-terminal extensions of α-crystallin and the N-terminal extension of βB2-crystallin are readily observed suggesting that these regions are not involved in crystallin-crystallin interactions. In the cortical homogenate, resonances from the short N-terminal extension of γS-crystallin are also present. The cortical homogenate gives rise to more intense resonances than the nuclear homogenate, suggesting that the cortical region has many more mobile crystallin regions. In both homogenates, the C-terminal extension of βB2-crystallin and the very short C-terminal extension of γB-crystallin are not observed. Thus, the C-terminal regions of these proteins are involved in interactions with other crystallins. Similar effects are observed upon mixing of the individual crystallins, e.g. the C-terminal extension of γB-crystallin is absent in spectra of mixtures of total γ-crystallin and high-molecular-weight β-crystallin aggregates (βH). Overall, the results are consistent with a short-range order for the crystallins within the lens.

α-Crystallin: molecular chaperone and protein surfactant

Bovine lens α-crystallin has recently been shown to function as a molecular chaperone by stabilizing proteins against heat denaturation (Horwitz, J. (1992) Proc. Natl. Acad. Sci. USA, 89, 10449–10453). An investigation, using a variety of physico-chemical methods, is presented into the mechanism of stabilization. α-Crystallin exhibits properties of a surfactant. Firstly, a plot of conductivity of α-crystallin versus concentration shows a distinct inflection in its profile, i.e., a critical micelle concentration (cmc), over a concentration range from 0.15 to 0.17 mM. Gel chromatographic and 1H-NMR spectroscopic studies spanning the cmc indicate no change in the aggregated state of α-crystallin implying that a change in conformation of the aggregate occurs at the cmc. Secondly, spectrophotometric studies of the rate of heat-induced aggregation and precipitation of alcohol dehydrogenase (ADH), β L- and γ-crystallin in the presence of α-crystallin and a variety of synthetic surfactants show that stabilization against precipitation results from hydrophobic interactions with α-crystallin and monomeric anionic surfactants. Per mole of subunit or monomer, α-crystallin is the most efficient at stabilization. α-Crystallin, however, does not preserve the activity of ADH after heating. After heat inactivation, gel permeation HPLC indicates that ADH and α-crystallin form a high molecular weight aggregate. Similar results are obtained following incubation of β L- and γ-crystallin with α-crystallin. 1H-NMR spectroscopy of mixtures of α- and β L-crystallin, in their native states, reveals that the C-terminus of βB2-crystallin is involved in interaction with α-crystallin. In the case of γ- and α-crystallin mixtures, a specific interaction occurs between α-crystallin and the C-terminal region of γ B-crystallin, an area which is known from the crystal structure to be relatively hydrophobic and to be involved in intermolecular interactions. The short, flexible C-terminal extensions of α-crystallin are not involved in specific interactions with these proteins. It is concluded that α-crystallin interacts with native proteins in a weak manner. Once a protein has become denatured, however, the soluble complex with α-crystallin cannot be readily dissociated. In the aging lens this finding may have relevance to the formation of high molecular weight crystallin aggregates.

Identification by 1H NMR spectroscopy of flexible C-terminal extensions in bovine lens α-crystallin

Two-dimensional 1H NMR spectroscopy of bovine eye lens α-crystallin and its isolated α A and α B subunits reveals that these aggregates have short and very flexible C-terminal extensions of eight (α A) and ten (α B) amino acids which adopt little preferred conformation in solution. Total α-crystallin forms a tighter aggregate than the isolated α A and α B subunit aggregates. Our results are consistent with a micelle model for α-crystallin quaternary structure. The presence of terminal extensions is a general feature of those crystallins, α and β, which form aggregates.

Glutamate kinase activity in Brevibacterium flavum: Relationship between L-proline and L-glutamine biosynthesis

Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis, in which an isopeptide bond is formed between the C-terminal Glu of LysW and an amino group of α-aminoadipate (AAA). The resulting LysW-γ-AAA is phosphorylated by LysZ to form LysW-γ-AAA phosphate, which is subsequently reduced to LysW-γ-aminoadipic semialdehyde (LysW-γ-AASA) through a reaction catalyzed by LysY. In this study, we determined the crystal structures of LysY from Thermus thermophilus HB27 (TtLysY) complexed with TtLysW-γ-AASA and TtLysW-γ-AAA, respectively. In both structures, the globular domain of TtLysW was recognized by positively charged residues on helix α9 and the β11-α10 loop of TtLysY through conformational changes. A mutational analysis confirmed that the interactions observed between TtLysY and TtLysW are important for the function of TtLysY. The extended LysW recognition loop and conserved arginine residue were identified as signatures to discriminate LysY from ArgC, which is involved in arginine biosynthesis. Combined with the previously determined TtLysZ·TtLysW complex structure, TtLysW may simultaneously bind TtLysZ and TtLysY. These structural insights suggest the formation of a TtLysWZY ternary complex, in which the flexible C-terminal extension of TtLysW promotes the efficient transfer of the labile intermediate from the active site of TtLysZ to that of TtLysY during the sequential reactions catalyzed by TtLysZY.