forthcoming articles in Acta Crystallographica Section D

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.

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

W. Zhong, H. P. Morgan, I. W. McNae, P. A. M. Michels, L. A. Fothergill-Gilmore and M. D. Walkinshaw

Synopsis: Magnesium bound to Trypanosoma brucei pyruvate kinase in the presence of the allosteric activator fructose bisphosphate, but 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 high affinity for the substrate.

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

G. Volkers, J. M. Damas, G. J. Palm, S. Panjikar, C. M. Soares and W. Hinrichs

Synopsis: 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 diffusion pathways.

Crystallographic data processing for free-electron laser sources

T. A. White, A. Barty, F. Stellato, J. M. Holton, R. A. Kirian, N. A. Zatsepin and H. N. Chapman

Synopsis: A processing pipeline for diffraction data acquired using the `serial crystallography' methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah.

Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices

T. Skarzynski

Synopsis: Recent developments in X-ray crystallographic hardware related to structural biology research are presented and discussed.

Structural and Functional Analyses of a Bacterial Homologue of Hormone-Sensitive Lipase from a Metagenomic Library

T. D. Ngo, B. H. Ryu, H. Ju, E. Jang, K. Park, K. K. Kim and T. D. Kim

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

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

M. Marcia, E. Humphris-Narayanan, K. S. Keating, S. Somarowthu, K. Rajashankar and A. M. Pyle

Synopsis: Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed.

Squeezing the most from every crystal: the fine details of data collection

T. Krojer, A. C. W. Pike and F. von Delft

Synopsis: This article gives an overview of techniques and procedures for efficient data collection at synchrotron sources.

Applications of molecular replacement to G protein coupled receptors

A. C. Kruse, A. Manglik, B. K. Kobilka and W. I. Weis

Synopsis: The use of molecular replacement in solving G protein-coupled receptors is discussed, with specific examples described in detail.

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

S. Correale, A. Ruggiero, R. Capparelli, E. Pedone and R. Berisio

Structure-based elucidation of the regulatory mechanism for aminopeptidase activity

H. M. Ta, S. Bae, S. Han, J. Song, T. K. Ahn, S. Hohng, S. Lee and K. K. Kim

Structural Basis of High-Order Oligomerization of the Cullin3 Adaptor, SPOP

L. K. van Geersdaele, M. A. Stead, C. M. Harrison, S. B. Carr, H. J. Close, G. O. Rosbrook, S. D. Connell and S. C. Wright

Synopsis: The crystal structure of a novel C-terminal dimerization domain of the cullin3 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

E. V. Soriano, Y. Zhang, K. L. Colabroy, J. M. Sanders, E. C. Settembre, P. C. Dorrestein, T. P. Begley and S. E. Ealick

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

Clustering procedures for the optimal selection of datasets from multiple crystals in macromolecular crystallography.

J. Foadi, P. Aller, Y. Alguel, A. Cameron, D. Axford, R. L. Owen, W. Armour, D. G. Waterman, S. Iwata and G. Evans

Synopsis: A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained.

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

C. Krintel, K. Harpsøe, L. G. Zachariassen, D. Peters, K. Frydenvang, D. S. Pickering, M. Gajhede and J. S. Kastrup

Synopsis: The crystal structures of the GluA2 LBD in complex with the positive allosteric modulator CX516 and its methyl substituted analogue Me-CX516 show that the binding modes are similar to that 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.

Fine-tuning of Proto-type Chicken Galectins: Crystal Structure of CG-2 and Structure-Activity Correlations

F. M. Ruiz, I. S. Fernández, L. López-Merino, L. Lagartera, H. Kaltner, M. Menéndez, S. André, D. Solís, H. Gabius and A. Romero

Structural and Functional Characterization of the N-terminal Domain of Yeast Mg²⁺ Channel Mrs2

M. B. Khan, G. Sponder, B. Sjöblom, S. Svidová, R. J. Schweyen, O. Carugo and K. Djinovic-Carugo

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

Half a century of Ramachandran plots

O. Carugo and K. Djinovic Carugo

Molecular replacement then and now

G. Scapin

Synopsis: A brief overview, with examples, of the evolution of molecular replacement methods and models over the past few years is presented

Structure Determination of an 11-Subunit Exosome in Complex with RNA by Molecular Replacement

D. L. Makino and E. Conti

Synopsis: The crystallographic steps towards the structure determination of a complete eukaryotic exosome complex bound to RNA are presented. Phasing of this 11-protein subunit complex was carried out via molecular replacement.

Visualization of membrane-protein crystals in the lipid cubic phase using X-ray imaging

A. J. Warren, W. Armour, D. Axford, M. Basham, T. Connolley, D. R. Hall, S. Horrell, K. E. McAuley, V. Mykhaylyk, A. Wagner and G. Evans

Synopsis: A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane-protein crystals mounted within lipid cubic phase material.

Structure of full-length human CTNNBL1 reveals a distinct member of the armadillo-repeat protein family

X. Huang, G. Wang, Y. Wu and Z. Du

Synopsis: The crystal structure of full-length human CTNNBL1 reveals many unique structural features that establish CTNNBL1 as a distinct member of the armadillo-repeat protein family.

Structure of the cobalamin-binding protein of a putative O-demethylase from Desulfitobacterium hafniense DCB-2

H. Sjuts, M. S. Dunstan, K. Fisher and D. Leys

Structural basis for intersubunit recognition in elongin BC-cullin 5-SOCS-box protein-ubiquitin ligase complexes

Y. K. Kim, M.-J. Kwak, B. Ku, H.-Y. Suh, K. Joo, J. Lee, J. U. Jung and B.-H. Oh

Synopsis: The crystal structure of the SOCS2-elongin BC-Cul5(1-386) complex explains the specificity of Cul2 and Cul5 for elongin BC and their preferential association with Cul2 or Cul5 box-containing proteins.

Structural and mechanistic studies of the orf12 gene product from the clavulanic acid biosynthesis pathway

K. Valegård, A. Iqbal, N. J. Kershaw, D. Ivison, C. Généreux, A. Dubus, C. Blikstad, M. Demetriades, R. J. Hopkinson, A. J. Lloyd, D. I. Roper, C. J. Schofield, I. Andersson and M. A. McDonough

Synopsis: Structural studies of the protein encoded by orf12 of the clavulanic acid biosynthesis gene cluster from S. clavuligerus reveal a two-domain structure.

Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata

M. Shankar, S. M. Wilbanks, Y. Nakatani, B. C. Monk and J. D. A. Tyndall

Synopsis: The crystal structure of lumazine synthase from C. glabrata complexed with its catalytic product 6,7-dimethyl-8-(D-ribityl)lumazine is reported.

Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor

F. Giannese, M. Berg, P. Van der Veken, V. Castagna, P. Tornaghi, K. Augustyns and M. Degano

Synopsis: The enzymatic and structural characterization of the drug target purine-specific nucleosidase from the pathogen T. brucei provides a rationale for the tight-binding inhibition by iminoribitol-based compounds. The binding of a metalorganic inhibitor to nucleoside hydrolases is reported for the first time, together with the structural basis of metal-mediated noncompetitive inhibition.

Invariom refinement of a new monoclinic solvate of thiostrepton at 0.64 Å resolution

K. Pröpper, J. J. Holstein, C. B. Hübschle, C. S. Bond and B. Dittrich

Synopsis: Structure refinement with nonspherical scattering factors from the invariom database is performed on thiostrepton, a heavily modified hexadecapeptide with antibiotic activity.

Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

T. R. M. Barends, R. W. W. Brosi, A. Steinmetz, A. Scherer, E. Hartmann, J. Eschenbach, T. Lorenz, R. Seidel, R. L. Shoeman, S. Zimmermann, R. Bittl, I. Schlichting and J. Reinstein

Synopsis: The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed.

Structural basis for the dephosphorylating activity of PTPRQ towards phosphatidylinositide substrates

K. R. Yu, Y. J. Kim, S.-K. Jung, B. Ku, H. Park, S. Y. Cho, H. Jung, S. J. Chung, K. H. Bae, S. C. Lee, B. Y. Kim, R. L. Erikson, S. E. Ryu and S. J. Kim

Structural asymmetry of procaspase-7 bound to a specific inhibitor

H. J. Kang, Y. Lee, K.-H. Bae, S. J. Kim and S. J. Chung

Hfq binds ribonucleotides in three different RNA-binding sites

V. Murina, N. Lekontseva and A. Nikulin

Synopsis: The ribonucleotide-binding properties of Hfq were probed using crystallography.

The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs

A. Sharma, G. Pohlentz, K. B. Bobbili, A. A. Jeyaprakash, T. Chandran, M. Mormann, M. J. Swamy and M. Vijayan

Synopsis: A novel three-chain nontoxic homologue of type II ribosome-inactivating proteins has been sequenced by mass spectrometry and its crystal structure has been determined. The evolutionary history of type II RIPs and the molecular basis for the loss of toxicity in some of them have been explored.

A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals

I. Nederlof, E. van Genderen, Y.-W. Li and J. P. Abrahams

Synopsis: An ultrasensitive Medipix2 detector allowed the collection of rotation electron-diffraction data from single three-dimensional protein nanocrystals for the first time. The data could be analysed using the standard X-ray crystallography programs MOSFLM and SCALA.

Microcrystal manipulation with laser tweezers

A. Wagner, R. Duman, A. Ward and B. Stevens

Synopsis: Optical trapping has successfully been applied to select and mount microcrystals for subsequent X-ray diffraction experiments.

Structure determination of the functional domain interaction of a chimeric nonribosomal peptide synthetase from a challenging crystal with noncrystallographic translational symmetry

J. A. Sundlov and A. M. Gulick

Mitigation of X-ray damage in macromolecular crystallography by submicrometre line focusing

Y. Z. Finfrock, E. A. Stern, R. W. Alkire, J. J. Kas, K. Evans-Lutterodt, A. Stein, N. Duke, K. Lazarski and A. Joachimiak

Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2

H. Liu, Y. Gao, M. Zhang, X. Qiu, A. J. L. Cooper, L. Niu and M. Teng

Synopsis: Structures of yeast Nit2 in complex with -ketoglutarate and with oxaloacetate revealed the molecular-recognition mechanism of the enzyme for the first time, while that of the C169S mutant of yeast Nit2 showed a new ligand located in the catalytic cavity.

On the reproducibility of protein crystal structures: five atomic resolution structures of trypsin

D. Liebschner, M. Dauter, M. Brzuszkiewicz and Z. Dauter

Synopsis: Details of five very high-resolution accurate structures of bovine trypsin are compared in the context of the reproducibility of models obtained from crystals grown under identical conditions.

Structural and catalytic characterization of a thermally stable and acid-stable variant of human carbonic anhydrase II containing an engineered disulfide bond

C. D. Boone, A. Habibzadegan, C. Tu, D. N. Silverman and R. McKenna

Trapped intermediates in crystals of the FMN-dependent oxidase PhzG provide insight into the final steps of phenazine biosynthesis

N. Xu, E. G. Ahuja, P. Janning, D. V. Mavrodi, L. S. Thomashow and W. Blankenfeldt

Synopsis: The structures of tricyclic intermediates trapped in crystals of PhzG suggest a basis for the chemistry and promiscuity of the final steps of phenazine biosynthesis.

MAIN software for density averaging, model building, structure refinement and validation

D. Turk

Synopsis: MAIN is interactive software designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. The features of MAIN and its tools for electron-density map calculations, model building, refinement in real and reciprocal space, and validation exploiting noncrystallographic symmetry in single and multiple crystal forms are presented.

Protein HP1028 from the human pathogen Helicobacter pylori belongs to the lipocalin family

N. Barison, L. Cendron, V. Loconte, E. A. Proctor, N. V. Dokholyan and G. Zanotti

Synopsis: The crystal structure of HP1028, a protein from the human pathogen H. pylori, demonstrates that it belongs to the lipocalin family.

Structures of an ATP-independent Lon-like protease and its complexes with covalent inhibitors

J.-H. Liao, K. Ihara, C.-I. Kuo, K.-F. Huang, S. Wakatsuki, S.-H. Wu and C.-I. Chang

Synopsis: The crystal structure of an ATP-independent LonC protease revealed a proteolytic chamber with two open axial pores. A LonC-specific N-terminal coil tethers the AAA+ and protease domains together. Structures with covalent inhibitors bound to the proteolytic active sites provide mechanistic insights into the recognition of inhibitors and polypeptide substrates within the conserved Lon proteolytic chamber.

Anatomy of secretin binding to the Dickeya dadantii type II secretion system pilotin

S. Rehman, S. Gu, V. E. Shevchik and R. W. Pickersgill

Synopsis: The crystal structure of the C-terminal peptide of secretin bound to the surface of its cognate pilotin reveals interactions that are essential for the assembly of a functional type II secretion system in D. dadantii and related secretion systems.

Tying down the arm in Bacillus dUTPase: structure and mechanism

J. García-Nafría, J. Timm, C. Harrison, J. P. Turkenburg and K. S. Wilson

Synopsis: Structures of the B. subtilis dUTPases in a novel complex with dU-PP_i-Mg²⁺ and in complex with dUMP provide insights into the mechanism and identify features unique to the B. subtilis enzymes.

The structure of an MDM2-Nutlin-3a complex solved by the use of a validated MDM2 surface-entropy reduction mutant

B. Anil, C. Riedinger, J. A. Endicott and M. E. M. Noble

Synopsis: The design, validation, proof of mechanism and exploitation of a surface-entropy reduction mutant to solve the structure of the benchmark inhibitor Nutlin-3a bound to the cancer drug-discovery target MDM2 are reported.

The use of a mini- goniometer head in macromolecular crystallography diffraction experiments

S. Brockhauser, R. B. G. Ravelli and A. A. McCarthy

Synopsis: Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented.

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