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The Keima family comprises large Stokes shift fluorescent proteins that are useful for dual-color fluorescence cross-correlation spectroscopy and multicolor imaging. The tKeima is a tetrameric large Stokes shift fluorescent protein and serves as the ancestor fluorescent protein for both dKeima and mKeima. The spectroscopic properties of tKeima have been previously reported; however, its structural basis and molecular properties have not yet been elucidated. In this study, we present the crystallographic results of the large Stokes shift fluorescent protein tKeima. The purified tKeima protein spontaneously crystallized after purification without further crystallization. The crystal structure of tKeima was determined at 3.0 Å resolution, revealing a β-barrel fold containing the Gln-Tyr-Gly chromophores mainly with cis-conformation. The tetrameric interfaces of tKeima were stabilized by numerous hydrogen bonds and salt–bridge interactions. These key residues distinguish the substituted residues in dKeima and mKeima. The key structure-based residues involved in the tetramer formation of tKeima provide insights into the generation of a new type of monomeric mKeima. This structural analysis expands our knowledge of the Keima family and provides insights into its protein engineering. [ABSTRACT FROM AUTHOR]

Endo-β-1,4-xylanases degrade heteroxylans that constitute the lignocellulosic plant cell wall. This enzyme is widely used in the food, paper, textile, and biorefinery industries. Temperature affects the optimum activity of xylanase and is an important factor in its application. Various structural analyses of xylanase have been performed, but its structural influence by temperature is not fully elucidated. To better understand the structural influence of xylanase due to temperature, the crystal structure of xylanase II from Trichoderma longibrachiatum (TloXynII) at room and cryogenic temperatures was determined at 2.1 and 1.9 Å resolution, respectively. The room-temperature structure of TloXynII (TloXynIIRT) showed a B-factor value 2.09 times higher than that of the cryogenic-temperature structure of TloXynII (TloXynIICryo). Subtle movement of the catalytic and substrate binding residues was observed between TloXynIIRT and TloXynIICryo. In TloXynIIRT, the thumb domain exhibited high flexibility, whereas in TloXynIICryo, the finger domain exhibited high flexibility. The substrate binding cleft of TloXynIIRT was narrower than that of TloXynIICryo, indicating a distinct finger domain conformation. Numerous water molecule networks were observed in the substrate binding cleft of TloXynIICryo, whereas only a few water molecules were observed in TloXynIIRT. These structural analyses expand our understanding of the temperature-dependent conformational changes in xylanase. [Display omitted] • The crystal structures of TloXynII at room and cryogenic temperatures were determined. • TloXynIIRT and TloXynIICryo exhibited different conformations for the catalytic and substrate-binding residues. • The substrate-binding cleft of TloXynIIRT was narrower than that of TloXynIICryo. • TloXynIIRT showed a B-factor value that was 2.09 times higher than that of TloXynIICryo. • The regions of higher flexibility differed between TloXynIIRT and TloXynIICryo. [ABSTRACT FROM AUTHOR]

β-glucosidases (Bgls) are glycosyl hydrolases that catalyze the conversion of cellobiose or glucosyl-polysaccharide into glucose. Bgls are widely used in industry to produce bioethanol, wine and juice, and feed. Tris (tris(hydroxymethyl)aminomethane) is an organic compound that can inhibit the hydrolase activity of some Bgls, but the inhibition state and selectivity have not been fully elucidated. Here, three crystal structures of Thermoanaerobacterium saccharolyticum Bgl complexed with the Tris molecule were determined at 1.55–1.95 Å. The configuration of Tris binding to TsaBgl remained consistent across three crystal structures, and the amino acids interacting with the Tris molecule were conserved across Bgl enzymes. The positions O1 and O3 atoms of Tris exhibit the same binding moiety as the hydroxyl group of the glucose molecule. Tris molecules are stably positioned at the glycone site and coordinate with surrounding water molecules. The Tris-binding configuration of TsaBgl is similar to that of HjeBgl, HgaBgl, ManBgl, and KflBgl, but the arrangement of the water molecule coordinating Tris at the aglycone site differs. Meanwhile, both the arrangement of Tris and the water molecules in ubBgl, NkoBgl, and SfrBgl differ from those in TsaBgl. The binding configuration and affinity of the Tris molecule for Bgl may be affected by the residues on the aglycone and gatekeeper regions. This result will extend our knowledge of the inhibitory effect of Tris molecules on TsaBgl. • Three crystal structures of Tris-bound T. saccharolyticum Bgl were determined. • Tris binding to the glycone site is stabilized by conserved active site residues and water interactions. • The similarities and differences in the Tris-binding configuration among various Bgl structures were analyzed. • Nonconserved aglycone and gatekeeper sites of Bgl may be involved in the recognition of Tris molecules. [ABSTRACT FROM AUTHOR]

Understanding the enzyme reaction mechanism is important for identifying fundamental biochemical processes and for providing invaluable information for enzyme engineering for industrial applications. Serial femtosecond crystallography (SFX) enables determination structure of enzymes without radiation damage at room temperature. Time-resolved SFX with ligand mixing provides a molecular movie of enzyme reactions, including the transition states. This structural information provides insight into previously undiscovered molecular dynamics over various time periods. To observe enzyme reactions with SFX, it is essential to comprehend the device used for mixing the protein crystals and reaction solutions, as well as the mixing efficiency and available time delay provided by this equipment. In this review, we summarize the current mixing techniques for time-resolved SFX. We describe the configuration and experimental setup of the SFX sample environment unique to each experimental technique and discuss the technical possibilities and limitations of these techniques for performing time-resolved crystallography. • Time-resolved mixing SFX experiments for enzyme reactions are explained. • Mixing devices and time-resolved mixing SFX results are summarized. • Potential available mixing devices for time-resolved SFX are discussed. • The possibilities and limitations of time-resolved mixing SFX are discussed. [ABSTRACT FROM AUTHOR]

Type I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets and the nuclease-helicase Cas3 to degrade them. Among the seven subtypes, type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here, we use four cryoelectron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9 that strongly inhibit Neisseria lactamica I-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through allosteric inhibition, whereas AcrIC9 achieves so through direct competition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for type I CRISPR eukaryotic genome engineering. [Display omitted] • Four cryo-EM snapshots reveal DNA capture and Cas3 activation for type I-C CRISPR • Cas3 is recruited via "handshaking" with Cascade to the full R-loop • AcrIC8 and AcrIC9 inhibit PAM recognition by I-C Cascade via distinct mechanisms • AcrIC8 and AcrIC9 provide off-switches for type I CRISPR gene editing in human cells Hu et al. elucidate the PAM recognition, R-loop formation, and Cas3 recruitment processes for type I-C CRISPR activation. Two anti-CRISPR proteins, AcrIC8 and AcrIC9, block PAM recognition by I-C Cascade via distinct mechanisms and can serve as off-switches for type I-C genome deletion and transcriptional activation applications in human cells. [ABSTRACT FROM AUTHOR]