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.

Accepted 26 May 2015

Structure of green fluorescent protein NowGFP with an anionic tryptophan-based chromophore

V. Z. Pletnev, N. V. Pletneva, K. S. Sarkisyan, A. S. Mishin, K. A. Lukyanov, E. A. Goryacheva, R. H. Ziganshin, Z. Dauter and S. Pletnev

Synopsis: Three-dimensional structure of green fluorescent protein NowGFP (succesor of Cerulean) with an anionic tryptophan-based chromophore and that of NowGFP_conv in the photoconverted form. Relation between structure and photophysical characteristics

Accepted 22 May 2015

Crystal structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate transfer mechanism

A. Mosale Venkatesh Murthy, S. Mathivanan, S. Chittori, H. S. Savithri and M. R. N. Murthy

Accepted 20 May 2015

Structural and adhesive properties of the long polar fimbriae protein LpfD from adherent invasive Escherichia coli

F. Coppens, J. Iyyathurai, S. Ruer, A. Fioravanti, J. Taganna, L. Vereecke, H. De Greve and H. Remaut

Synopsis: The LpfD protein represents the tip adhesin of enterobacteriaceal Long Polar Fimbriae and LpfD of the adherent invasive E. coli strain LF82 directs LPF binding towards the intestinal epithelium and underlying tissue.

Accepted 18 May 2015

Structural basis of deerpox virus-mediated inhibition of apoptosis

D. R. Burton, S. Caria, B. Marshall, M. Barry and M. Kvansakul

Synopsis: Deerpoxvirus employs the cell death inhibitor DPV022 to prevent premature host cell death by engaging pro-death Bcl-2 proteins via two independent ligand binding sites as part of a domain-swapped Bcl-2 fold.

Accepted 18 May 2015

High-resolution crystal structures of the solubilized domain of porcine cytochrome b5

Y. Hirano, S. Kimura and T. Tamada

Synopsis: The crystal structures of the solubilized domain of cytochrome b5 from porcine liver were determined at sub-Â resolutions in two crystal forms for both the oxidized and reduced states. The high-resolution structures provided information about factors important for regulating the electronic properties of the heme group of cytochrome b5.

Accepted 18 May 2015

High-resolution crystal structure of phosphatidylinositol 4-kinase II[beta] and crystal structure of phosphatidylinositol 4-kinase II[alpha] containing a nucleoside analogue provide the structural basis for isoform-specific inhibitor design

M. Klima, A. Baumlova, D. Chalupska, H. Hrebabecký, M. Dejmek, R. Nencka and E. Boura

Synopsis: The crystal structure of the phosphatidylinositol 4-kinase (PI4K) II[beta] reveals new details such as the high conformational heterogeneity of the lateral hydrophobic pocket, and, together with the structure of PI4K II[alpha] with a nucleoside analogue, provides structural basis for isoform-specific inhibitor design.

Accepted 15 May 2015

Enantioselective oxidation of galactitol-1-phosphate by galactitol-1-phosphate 5-de­hydrogenase from Escherichia coli

R. Benavente, M. Esteban-Torres, G.-W. Kohring, Á. Cortés-Cabrera, P. Sánchez-Murcia, F. Gago, I. Acebrón, B. de las Rivas, R. Muñoz and J. M. Mancheño

Synopsis: Three crystal structures of L-galactitol-1-phosphate 5-dehydrogenase from Escherichia coli have been solved. The functional data were combined with the structural results to understand the enantioselectivity of this enzyme.

Accepted 15 May 2015

Structure of the Catalytic Phosphatase Domain of MTMR8: Implications for Dimerization, Membrane Association, and Reversible Oxidation

K.-Y. Yoo, J. Y. Son, J. U. Lee, W. Shin, D.-W. Im, S. J. Kim, S. E. Ryu and Y.-S. Heo

Synopsis: The crystal structure of the phosphatase domain of MTMR8 provides insights into its dimerization, membrane association, and reversible regulation.

Accepted 15 May 2015

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

S. M. Arif, K. Geethanandan, P. Mishra, A. Surolia, U. Varshney and M. Vijayan

Synopsis: Seventeen independent crystal structures of family I uracil-DNA glycosylase from M. tuberculosis (MtUng) and their complexes with uracil and its derivatives, distributed among five distinct crystal forms, provide information on conformational selection on DNA binding, segmental mobility and protein-ligand interactions.

Accepted 14 May 2015

Synopsis From bacterial to human di­hydrouridine synthase: automated structure determination

F. Whelan, H. T. Jenkins, S. C. Griffiths, R. T. Byrne, E. J. Dodson and A. A. Antson

Synopsis: The crystal structure of a human dihydrouridine synthase, an enzyme associated with lung cancer, with 18% sequence identity to a Thermatoga maritima enzyme has been determined at 1.9 Å resolution by molecular replacement after extensive molecular remodelling of the template.

Accepted 14 May 2015

Structural and biochemical analyses of a Clostridium perfringens Sortase D transpeptidase

R. Suryadinata, S. A. Seabrook, T. E. Adams, S. D. Nuttall and T. S. Peat

Synopsis: The structure of Clostridium perfringens Sortase D was determined at 1.99 Å resolution. Comparative biochemical and structural analyses revealed that this transpeptidase may represent a new subclass of the Sortase D family.

Accepted 6 May 2015

Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein

S. Klingl, M. Scherer, T. Stamminger and Y. A. Muller

Synopsis: Controlled dehydration of IE1 crystals leads to molecular rearrangements that trigger a space-group transition from P21 to P43 with a concomitant reduction of the number of IE1 chains in the asymmetric unit. Analysis of the pre- and post-dehydration structures reveals a reshaping of the tertiary structure of IE, which possibly informs on the mechanism by which IE1 binds to host-cell target proteins.

Accepted 30 April 2015

Structure of protease-cleaved Escherichia coli [alpha]-2-macroglobulin reveals a putative mechanism of conformational activation for protease entrapment

C. D. Fyfe, R. Grinter, I. Josts, K. Mosbahi, A. Roszak, R. J. Cogdell, D. M. Wall, R. J. S. Burchmore, O. Byron and D. Walker

Synopsis: The X-ray structure of protease-cleaved Escherichia coli [alpha]-2-macroglobulin is described, which reveals a putative mechanism of activation and conformational change essential for protease inhibition.

Accepted 27 April 2015

Detection of trans-cis flips and peptide-plane flips in protein structures

W. G. Touw, R. P. Joosten and G. Vriend

Synopsis: A method is presented to detect peptide bonds that need either a trans-cis flip or a peptide-plane flip.

Accepted 27 April 2015

Intercalating dyes for enhanced contrast in second-harmonic generation imaging of protein crystals

J. A. Newman, N. M. Scarborough, N. R. Pogranichniy, R. K. Shrestha, R. G. Closser, C. Das and G. J. Simpson

Synopsis: The intercalation of SHG active dyes into formed protein crystals has allowed the enhancement of second-harmonic generation signal from protein crystals by ~1000-fold.

Accepted 22 April 2015

Defined PEG smears as an alternative approach to enhance the search for crystallization conditions and crystal-quality improvement in reduced screens

A. Chaikuad, S. Knapp and F. von Delft

Accepted 21 April 2015

New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM

F. Fadel, Y. Zhao, R. Cachau, A. Cousido-Siah, F. X. Ruiz, K. Harlos, E. Howard, A. Mitschler and A. Podjarny

Accepted 20 April 2015

Protonation and geometry of histidine rings

M. Malinska, M. Dauter, M. Kowiel, M. Jaskolski and Z. Dauter

Synopsis: The correlation of histidine-ring geometry with the protonation state was analyzed in structures in the PDB and CSD. In conclusion, revised stereochemical restraints for histidine are proposed.

Accepted 18 April 2015

A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens

C. Y. Koh, L. Kallur Siddaramaiah, R. M. Ranade, J. Nguyen, T. Jian, Z. Zhang, J. R. Gillespie, F. S. Buckner, C. L. M. J. Verlinde, E. Fan and W. G. J. Hol

Synopsis: A crystallographic cocktail screening campaign against 680 fragments revealed a binding hotspot in the structure of T. cruzi histidyl-tRNA synthetase.

Accepted 17 April 2015

S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations

S. Klinke, N. Foos, J. J. Rinaldi, G. Paris, F. A. Goldbaum, P. Legrand, B. G. Guimarães and A. Thompson

Synopsis: The structure of the histidine kinase associated with the light-oxygen-voltage domain from B. abortus, containing 968 amino acids in the asymmetric unit, was solved using the `off-edge' anomalous signal from sulfur to a resolution of 2.90 Å by combining data from several isomorphous crystals (space group P21) as well as data collected from multiple orientations of the same crystal (true redundancy), stressing the importance of the latter approach in off-edge S-SAD. A second construct that has a shorter cloning artifact enabled the production of improved crystals and subsequent refinement of the structure to 2.51 Å resolution.

Accepted 15 April 2015

Predicting X-ray diffuse scattering from translation-libration-screw structural ensembles

A. H. Van Benschoten, P. V. Afonine, T. C. Terwilliger, M. E. Wall, C. J. Jackson, N. K. Sauter, P. D. Adams, A. Urzhumtsev and J. S. Fraser

Synopsis: A method of simulating X-ray diffuse scattering from multi-model PDB files is presented. Despite similar agreement with Bragg data, different translation-libration-screw refinement strategies produce unique diffuse intensity patterns.

Accepted 15 April 2015

Two high-mobility group box domains act together to underwind and kink DNA

R. Sánchez-Giraldo, F. J. Acosta-Reyes, C. S. Malarkey, N. Saperas, M. E. A. Churchill and J. L. Campos

Synopsis: The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure.

Accepted 10 April 2015

Protein secondary-structure description with a coarse-grained model

G. R. Kneller and K. Hinsen

Synopsis: A generalization of the ScrewFit method for protein secondary-structure description and analysis is presented which uses only the positions of the C[alpha] atoms and describes the winding of the protein main chain as a succession of screw motions which link consecutive residue-based Frenet frames on the discrete C[alpha] space curve.

Accepted 27 March 2015

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin

I. Shabalin, Z. Dauter, M. Jaskolski, W. Minor and A. Wlodawer

Synopsis: Models of crystal structures deposited in the Protein Data Bank for protein complexes of cisplatin and carboplatin appear to have troubling crystallographic problems and to exhibit significant departures from the known principles of chemistry. They may serve as examples of what should be improved in the deposition and presentation of macromolecular models and how to handle deposition of the results of re-refinement of crystallographic data.

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