The crystal structure reveals the molecular mechanism of bifunctional 3,4-di­hydroxy-2-butanone 4-phosphate synthase/GTP cyclo­hydrolase II (Rv1415) from Mycobacterium tuberculosis

This study represents the first crystal structure of bi-functional ribB/ribA enzyme from Mycobacterium tuberculosis.

Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain

The crystal structures of the GluA2 ligand-binding domain in complex with the positive allosteric modulator CX516 and its methyl-substituted analogue Me-CX516 show that their binding modes are similar to those of aniracetam and CX614. This supports that CX516 affects receptor deactivation. The structures also show that there is limited space for substitutions at the piperidine ring of CX516.

Structural and functional characterization of the N-terminal domain of the yeast Mg²⁺ channel Mrs2

The first structure of the N-terminal domain of the Mg²⁺ channel Mrs2 in a monomeric form and a pentameric model of Mrs2 generated using the prokaryotic homologue CorA are presented. Gating and metal-sensing residues were proposed based on the model and were validated using mutational and functional studies in vivo.

Fine-tuning of prototype chicken galectins: structure of CG-2 and structure–activity correlations

Expression profiling of the three homodimeric (prototype) chicken galectins (CG-1A, CG-1B and CG-2) has raised evidence of distinct functionalities, explaining the interest in a detailed crystallographic analysis of CG-2. Marked differences are found in the ligand-binding site and in the contact pattern within the homodimer interface, underlying a characteristic orientation of the two subunits. Notably, a distinctive trimer of dimers that is unique in all galectin crystal structures reported to date forms the core unit of the crystallographic assembly.

Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP

The crystal structure of a novel C-terminal dimerization domain of the cullin-3 adaptor SPOP is reported. The dimerization interfaces of the SPOP BTB and C-terminal domains act in tandem to generate high-order oligomers that enhance the ubiquitination of substrates.

Active-site models for complexes of quinolinate synthase with substrates and intermediates

Structural studies of quinolinate synthase suggest a model for the enzyme–substrate complex and an enzyme–intermediate complex with a [4Fe–4S] cluster.

Structures of free and inhibited forms of the L,D-transpeptidase Ldt_Mt1 from Mycobacterium tuberculosis

This work reports the crystal structures of the L,D-transpeptidase Ldt_Mt1 from M. tuberculosis in a ligand-free form and in complex with the carbapenem imipenem.

Structure of the AvrBs3–DNA complex provides new insights into the initial thymine-recognition mechanism

The crystal structure of the AvrBs3–DNA complex is reported.

The structure of XIAP BIR2: understanding the selectivity of the BIR domains

The high-resolution crystal structures of apo and peptide-bound XIAP BIR2 are presented and compared with BIR3 structures to understand their selectivity. This crystal system can be used to determine the structures of BIR2–inhibitor complexes.

Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library

The crystal structure of Est25, a bacterial homologue of hormone-sensitive lipase (HSL), was determined at 1.49 Å resolution. The biochemical properties of Est25 were investigated to clarify the functional capacities of HSL and the potential applications of Est25 in biotechnology.

Structure-based elucidation of the regulatory mechanism for aminopeptidase activity

Crystallographic, functional and single-molecule studies of aminopeptidase PepS have been presented. Substrate length selectivity imposed by the substrate binding hole is a key in the regulation of the catalytic activity along with residue specificity and active-site repositioning.

1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein

Diffraction analysis of E. coli WrbA crystallized in the presence of FAD yields the highest resolution structure yet reported, but with FMN bound, Met10 oxidized, and a propeller-twisted isoalloxazine ring.

Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX

Crystal structure analyses of the monooxygenase TetX in complex with tigecycline and minocycline support the observation that all clinically available tetracycline antibiotics can be inactivated by enzymatic hydroxylation. Molecular-dynamics simulations of dioxygen diffusion and experimental xenon-binding sites in TetX are compared with respect to putative dioxygen-binding cavities and dioxygen-diffusion pathways.

`In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase

Magnesium bound to T. brucei pyruvate kinase in the presence of the allosteric activator fructose bisphosphate, but in the absence of the substrate phosphoenolpyruvate, is sequestered in a previously undescribed `priming' position adjacent to the active site. In this way, the enzyme is kept in a conformation with a high affinity for the substrate.

Analysis of the human cofilin 1 structure reveals conformational changes required for actin binding

The crystal structure of the human actin-regulating protein cofilin 1, and comparisons with yeast, Chromalveolata and plant homologues that reveal conformational changes required for actin binding, are reported.

The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones

The crystal structure of the intact substrate-recognition domain of a LonC protease shows a large helical hairpin extension (HHE). The HHEs form a basket-like structure on top of the degradation chamber of the LonC protease. The HHE of LonC shares structural and functional similarity to the α-helical tentacle of the periplasmic chaperone Skp.

High-affinity inhibitors of Zymomonas mobilis tRNA–guanine transglycosylase through convergent optimization

The simultaneous filling of the ribose-33 and ribose-34 pockets at the active site of Z. mobilis tRNA–guanine transglycosylase was investigated using a series of bifunctionalized lin-benzopurine inhibitors. A strong influence of the crystallization protocol on the solvation pattern and the residual mobility of the bound ligands was observed in the cocrystal structures.

Structure of the inositol-1-phosphate cytidylyltransferase from Thermotoga maritima

The T. maritima inositol-1-phosphate cytidylyltransferase structure provides insights into its mechanism of forming CDP-inositol and its interaction with the membrane-bound enzyme in the next step of the biosynthesis of the unusual osmolyte di-myo-inositol-1,1′-phosphate in hyperthermophiles.

Peculiarity in crystal packing of anti-HIV lectin actinohivin in complex with α(1–2)mannobiose

The fully mature anti-HIV lectin actinohivin in complex with the target α(1–2)mannobiose moiety of the high-mannose-type glycans attached to HIV-1 gp120 has been crystallized into two new forms without packing disorder and their X-ray structures reveal the detailed interaction geometry for specific binding to the target HIV-1.

The structure of human α-2,6-sialyltransferase reveals the binding mode of complex glycans

The first structure of a human β-galactoside α-2,6-sialyltransferase I was determined by SIRAS phasing using an iodide soak for derivatization. An elongated glycan from a crystallographic neighbour binds to the active site, mimicking a substrate complex. An analysis of the substrate interactions and a comparison with other sialyltransferases allowed the modelling of a Michaelis complex and conclusions on the catalytic mechanism.

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

A new crystal-mounting method has been developed that involves a combination of controlled humid air and polymer glue for crystal coating. This method is particularly useful when applied to fragile protein crystals that are known to be sensitive to subtle changes in their physicochemical environment.

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59.

mrtailor: a tool for PDB-file preparation for the generation of external restraints

mrtailor is a tool to improve PDB files for the generation of external restraints for refinement.

Metal–ligand geometry relevant to proteins and in proteins: sodium and potassium. Corrigendum

A correction is made to the article by Harding [(2002) Acta Cryst. D58, 872–874].