The following articles are a selection of those recently accepted for publication in Acta Crystallographica Section D: Biological Crystallography.
See also Forthcoming articles in all IUCr journals.
Synopsis: In order to clarify the structural basis of halophilic characteristics of an alkaline phosphatase derived from the moderate halophile Halomonas sp.593 (HaAP), the tertiary structure of HaAP was determined to 2.1 Å resolution by X-ray crystallography. Structural properties of surface negative charge and core hydrophobicity are shown to be intermediate between halophile and non-halophile characteristics, and may explain the unique functional adaptation to a wide-range of salt concentration.
Synopsis: The structure of Rv2372c of M. tuberculosis reveals it as an RsmE-ortholog that belongs to a distinct class of SPOUT-superfamily and can complement RsmE-deleted E. coli cells.
Synopsis: Polyfluorinated compound 2,2',3,3',5,5',6,6'-octafluoro-4,4'-biphenyldiol (JF0064) is a potent inhibitor (IC50 1 µM) of both AR and AKR1B10. X-ray structures of both ternary complexes with JF0064 allow to infer that this lead compound binds to the enzyme active site through an acidic phenol group and to extract important hints for structure-based drug design.
Synopsis: A metal-independent glutaminyl cyclase from the black-legged tick Ixodes scapularis is reported. The metal-independent inhibition of QCs by the imidazole-derived inhibitors is described for the first time.
Synopsis: Structural insights of Leishmania major Farnesyl diphosphate synthase, a key enzyme in the mevalonate pathway.
Synopsis: In the present study, we determined the crystal structures of the multicopper oxidases and found the O (inside) structural feature at the trinuclear copper center.
Synopsis: The structure of a spore photoproduct lesion in duplex DNA is described.
Synopsis: The crystal structure of the class C extended-spectrum cepahalosporinase ADC-1 has been solved to 1.2 Å resolution.
Synopsis: The enzyme porphobilinogen deaminase (PBGD) (hydroxymethylbilane synthase; EC 184.108.40.206) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. We report two near-atomic resolution structures of the PBGD from B. megaterium that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor including one that possesses a tetrahedral carbon atom in the terminal pyrrole ring.
Synopsis: Ensemble refinement analysis of native and mutant FD crystal structures indicates a dynamical transition in FD from self-inhibited inactive to substrate-bound active that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles.
Synopsis: Catalytic antibody variants with and light constant domains show differences in their crystal structures, which lead to subtle changes in catalytic efficiency and thermodynamic parameters as well as in affinity for peptide substrates.
Synopsis: The crystal structures of the Y138F obelin mutant before and after bioluminescence reaction have been determined at 1.72 Å and 1.30 Å resolutions, respectively. Their spatial structures support the catalytic function of a water molecule found in an internal cavity in the light emission reaction of Ca2+-regulated photoproteins.
Synopsis: The crystal structures of the full-length Escherichia coli quorum sensing receptor SdiA revealed that it forms a symmetrical dimer and exhibits broad ligand-binding selectivity. The ligand binding increases the stability of SdiA but does not modulate the DNA-binding ability of SdiA. SdiA DNA-binding activity can be regulated through the formation of an intersubunit disulfide bond.
Synopsis: Substitutive mutations that convert a tetrameric -glucosidase into a dimeric state lead to improve its crystal-quality.
Synopsis: The structure of peptide - peptoid analog inhibitor was determined by X-ray crystallography. It is a first structure that reveals structural basis of complete proteolytic resistance toward serine proteases by inhibitors containing peptoid residue at P1 position.
Synopsis: Low activity mutant of a cold-adapted chitinase from Moritella marina has been crystallized and examined in an unliganded form and in complex with four and five N-acetyl-d-glucosamine units to reveal its substrate binding mode. The oligomerization and conformational flexibility of this multi-domain protein has also been examined in solution.
Synopsis: Using an extended set of protein features calculated separately for protein surface and interior, a new version of XtalPred based on Random Forest classifier achieves a significant improvement in predicting success of structure determination from the primary amino acid sequence.
Synopsis: Two crystal forms of unligated FKBP12.6 exhibit multiple conformations in the active site and in the 80's loop, primary site for known protein recognition interactions. The previously unreported NMR backbone assignment of FKBP12.6 revealed extensive doubling of amide resonances which reflects a slow conformational transition centered in the 80's loop.
Synopsis: This paper presents a novel and simple protein crystallization method called the Cross-Diffusion Microbatch (CDM) method. This method can dramatically increase the number of crystallization conditions and is a potentially useful technique in practical protein crystallization screening.
Synopsis: Information theory is used to estimate the precision of reported protein coordinates in the PDB.
Synopsis: Binding modes of acivicin, a classical and an electrophilic active-site directed glutamate analogue, to bacterial -glutamyltranspeptidases were diverse.
Synopsis: Crystal structure of the PLpro C112S mutant in complex with Ub offers insight into the molecular basis of the PLpro catalytic mechanism and its substrate binding. An N-cyclohexyl-2-aminethanesulfonic acid in the active site suggests a possible inhibiting approach.
Synopsis: The reduction reaction of different substrates by azoreductase has been investigated based on the crystal structures of AzrA and AzrC-inhibitor/substrate complexes. The structures of the AzrC-substrate complexes present two different manners of binding, suggesting two types of reduction reaction depending on the type of substrate.
Synopsis: The principles of the Bürgi-Dunitz nucleophilic approach necessitate structural rearrangements in Schiff-base-forming enzymes. Presented as a case study, substrate- and reaction intermediate-bound crystal complexes reveal that substrate conformational changes achieve the required rearrangements in transaldolase Schiff-base formation.
Synopsis: High-resolution crystal structures together with mutational analysis and transient kinetics experiments were utilized to understand nucleotide sensing and the regulation of the ATPase cycle in an AAA+ molecular motor.
Synopsis: High-resolution crystal structures of mitochondrial and cytosolic 5'-deoxyribonucleotidases with active-site phosphate ions were used to estimate phosphate protonation and to investigate differences in their active sites. These findings were applied to the design of a putative specific inhibitor.
Synopsis: With the implementation of a molecular-replacement likelihood target that accounts for translational noncrystallographic symmetry, it became possible to solve the crystal structure of a protein with seven tetrameric assemblies arrayed translationally along the c axis. The new algorithm found 56 protein molecules in reduced symmetry (P1), which was used to resolve space-group ambiguity caused by severe twinning.
Synopsis: The crystal structure of the Cmr1 subunit of the Cmr interference complex reveals a single-stranded RNA-binding site and an associated ribonuclease activity.
Synopsis: The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex are reported.
Synopsis: We made available a local raw 'diffraction data images' archive and some data sets were retrieved and reprocessed, which led to analysis of anomalous difference densities of two partially occupied chlorine atoms in cisplatin as well as the re-evaluation of resolution cut off in these diffraction data. We discuss general questions on storing raw data. We also demonstrate that often one needs unambiguous prior knowledge to read the (binary) detector format and the set-up of goniometer geometries.
Synopsis: The expression of carbohydrate-active proteins from C. thermocellum is proposed to be regulated by a I/anti-I (RsgI) mechanism that is sensitive to extracellular carbohydrates. Here, the structures of three putative RsgI carbohydrate-sensing modules belonging to the family 3 carbohydrate-binding modules are described.
Synopsis: The crystal structure of choline oxidase in complex with the physiological product glycine betaine allows comparison with previous mechanistic studies of choline oxidase and highlights a distinct conformation of a loop at the dimer interface which is suggested to regulate substrate access to the active site.
Synopsis: The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily.
Synopsis: Conformational differences between myoglobin structures are studied. Most structural differences in whale myoglobin beyond the uncertainty threshold can be correlated with a few specific structural factors. There are always exceptions and a search for additional factors is needed. The results might have serious implications for biological insights from conformational differences.
Synopsis: The structural and biochemical study of Kif15 provides insight into this potential drug target and allows comparison with Eg5, a kinesin that partially shares the functions of Kif15.
Synopsis: Co-crystals of SKF86002, a small kinase inhibitor, and various kinases were distinguishable by their strong fluorescence, and the crystals lost their fluorescence when a compound bound competitively to the kinase ATP-binding site and displaced the fluorescent SKF86002. SKF86002 binds a wide variety of kinases and thus would be a useful crystal marker, crystal stabilizer and marker for screening new kinase inhibitors and identifying ligand co-crystals for structural analysis.
Synopsis: A hybrid approach to the analysis of small-angle scattering data is presented, allowing determination of the orientation of bacteriorhodopsin reconstituted into a phopholipid nanodisc. The method is applicable to similar systems.
Synopsis: The Salmonella effector protein GtgE functions as a cysteine protease to cleave a subset of the Rab-family GTPases and to prevent delivery of antimicrobial agents to the Salmonella-containing vacuole.
Synopsis: The crystal structure of the serine acetyl-xylooligosaccharide esterase from G. stearothermophilus (Axe2) has been determined by SAD techniques, allowing full structural analysis of the selenomethionine derivative Axe2-Se (at 1.70 Å resolution), the wild type Axe2-WT (1.85 Å) and the catalytic mutant Axe2-S15A (1.90 Å). The structures show that the enzyme forms a unique octameric torus built of two staggered cyclic tetramers, with four pairs of catalytic triads facing the central cavity. This octameric torus is further confirmed by gel-filtration, TEM and SAXS results.
Synopsis: The structure of the human myelin peripheral membrane protein P2 has been refined at 0.93 Å resolution. In combination with functional experiments in vitro, in vivo and in silico, the fine details of the structure-function relationships in P2 are emerging.
Synopsis: The structure of a crystal of MPK38 (T167E), which consists of a kinase domain and a UBA domain, in complex with AMP-PNP is reported at 2.4 Å resolution. The structure indicates that the activation of MPK38 is induced by the UBA linker restraining the motion of the C helix and by phosphorylation of Thr167 stabilizing the activation loop.
Synopsis: Four crystal structures of S. cerevisiae CK2 (scCK2) with different nucleotide co-substrates and coordinated divalent cations indicated that scCK2 possesses dual co-substrate specificity, possible multiple nucleotide-divalent cation binding modes and a possible ADP/GDP-release pathway by means of conformational change of 1/G-loop/2. The presence of a unique insertion loop in scCK2 enhanced the catalytic efficiency of the enzyme by stabilizing the open conformation of the catalytic site.
Synopsis: This study describes the three-dimensional structure of the endogenous glycosylated allergen Hev b 2 (endo--1,3-glucanase), which exhibits three post-translational modifications that form a patch on the surface of the molecule that is proposed to be an allergenic IgE epitope.
Synopsis: This study presents the crystal structure of a 320 Å long protein fiber generated by in-frame extension of its repeated helical coiled-coil core.
Synopsis: Specifically deuterated phospholipid bilayer nanodiscs have been developed which give a minimal contribution to neutron scattering data when used in 100% D2O. These provide an optimal platform for low-resolution structural determination of membrane proteins and their complexes in solution.
Synopsis: A software system for automated protein-ligand crystallography has been implemented in the PHENIX suite. This significantly reduces the manual effort required in high-throughput crystallographic studies.
Synopsis: The crystal structure of a complex of full-length Arp7 and Arp9 was determined that shows that they form a heterodimer, in contrast to the monomeric units observed for other actin-related proteins. Therefore, the dimeric Arp7-Arp9 form that purportedly exists in the SWI/SNF and RSC chromatin-remodelling factors exists independently of the binding of other proteins in these megadalton complexes.
Synopsis: The structure of a bacterial M14-family carboxypeptidase determined exploiting microfocus synchrotron radiation and highly automated refinement protocols reveals its potential to act as a polyglutamylase.
Synopsis: FABP5 was recently found to intracellularly transport endocannabinoid signaling lipids. The structures of FABP5 complexed with two endocannabinoids and an inhibitor were solved. Human FABP5 was found to dimerize via a domain-swapping mechanism. This work will help in the development of inhibitors to raise endocannabinoid levels.
Synopsis: In this study, crystal structures of the E. coli Mre11 homologue SbcD and its Mn2+ complex are reported and an ssDNA-binding model is proposed for SbcD that differs from those of other Mre11 proteins, providing insight into the catalytic mechanism of the repair of DNA double-strand breaks by the Mre11 complex.
Synopsis: Refinement and analysis of four structures with various data resolution cutoffs suggests that at present there are no reliable criteria for judging the diffraction data resolution limit and the condition I/(I) = 2.0 is reasonable. However, extending the limit by about 0.2 Å beyond the resolution defined by this threshold does not deteriorate the quality of refined structures and in some cases may be beneficial.
Synopsis: Crystal structures of the H. pylori methylthioadenosine nucleosidase (MTAN) HpyMqnB have been solved in native and complexed forms, shedding light on substrate binding and the reaction mechanism.
Synopsis: Crystal structures of FbpA from T. thermophilus (TtFbpA) in its apo and ferric ion-bound forms have been solved. TtFbpA shows the novel formation of a six-coordinated complex of ferric ion coordinated by three tyrosine residues, two monodentate bicarbonates and a water molecule.
Synopsis: Vapour soaking of crystals of the R. rhodochrous haloalkane dehalogenase variant DhaA31 with 1,2,3-trichloropropane at room temperature and pH 6.5 facilitated the production of a protein-substrate complex. Comparison of the substrate-free DhaA31 structure with that of the DhaA31-substrate complex revealed two alternative conformations of the nucleophilic residue Asp106 and a possible pathway for halide release, while comparison of DhaA31 with wild-type DhaA revealed reduced size and solvent-accessibility of the active site.
Synopsis: The structures of human squalene synthase and its mutants in complex with several substrate analogues and intermediates coordinated with Mg2+ or Mn2+ stepwise delineate the biosynthetic pathway.
Synopsis: The FP domain of the human F-box protein Fbxo7 adopts an /-fold structure that is similar to the FP domain of the human proteasome inhibitor PI31. However, the two FP domains show dramatic differences in the way that they mediate protein-protein interactions.
Synopsis: In serial crystallography, it is demonstrated that the indexing mode of partial data sets can be established using correlation coefficients against other data sets and a clustering procedure. For 24 chiral space groups clustering can be performed in two dimensions, but in space groups P3, P31 and P32 clustering in three or four dimensions is required.
Synopsis: The structure of glutaredoxin 1 from P. falciparum has been determined at atomic resolution and its unique structural features have been dissected.
Synopsis: Letter to the editor.
Synopsis: An analysis of the rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP is presented.
Synopsis: The crystal structure of NleC is reported at 1.55 Å resolution. In conjunction with biochemical analyses, the structure reveals that NleC is a member of the zincin zinc protease family and that the configuration of the NleC active site resembles that of the metzincin clan of metallopeptidases.
Synopsis: Novel bent conformations of the calmodulin central helix are presented. The structures may relate to the initial stages of structural collapse in calmodulin upon target-peptide binding.
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