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.

High-resolution structure of Bombyx mori lipoprotein 7: crystallographic determination of protein's identity and potential role in detoxification

A. J. Pietrzyk, S. Panjikar, A. Bujacz, J. Mueller-Dieckmann, M. Lochynska, M. Jaskolski and G. Bujacz

Synopsis: Three crystal structures of a lipoprotein (Bmlp7) of unknown function, a member of the 30-kDa lipoprotein family of mulberry silkworm (Bombyx mori L.) hemolymph have been determined. The hemolymph-isolated protein was identified through successful sequence assignment according to electron density maps at 1.33 Å resolution.

Spatial distribution of radiation damage to crystalline proteins at 25 to 300 K

M. Warkentin, R. Badeau, J. B. Hopkins and R. E. Thorne

Synopsis: Dose-dependent atomic B-factors are used to determine the average spatial distribution of radiation damage to crystalline thaumatin and urease.

Detection of alternative conformations by unrestrained refinement

O. V. Sobolev and V. Y. Lunin

Synopsis: The values of atomic shifts in unrestrained refinement can hint alternative conformations.

Continuous -Turn Fold of an Alternating Alanyl/Homoalanyl Peptide Nucleic Acid

J. A. Cuesta-Seijo, J. Zhang, U. Diederichsen and G. M. Sheldrick

Synopsis: The 1.0 Å crystal structure of an alternating L-homoalanyl, D-alanyl PNA reveals a novel tetrameric cage with Watson-Crick pairing of the stacked nucleobases.

STRUCTURAL AND FUNCTIONAL STUDIES OF REP1-NCXSQ, A PROTEIN REGULATING THE SQUID NERVE Na⁺/Ca²⁺ EXCHANGER

A. Cousido-Siah, D. Ayoub, G. Berberián, M. Bollo, A. Van Dorsselaer, F. Debaene, R. DiPolo, T. Petrova, C. Schulze-Briese, V. Olieric, A. Esteves, A. Mitschler, S. Sanglier-Cianférani, L. Beaugé and A. Podjarny

Synopsis: Structural and functional studies show the importance of palmitic acid transport by the cytosolic protein ReP1-NCXSQ in the regulation of the squid nerve Na⁺/Ca²⁺ exchanger NCXSQ1 Abbreviation footnotes: ReP1-NCXSQ, cytosolic regulatory protein of the squid nerve Na⁺/Ca²⁺ exchanger; CRABP, cellular retinoic acid binding protein; FABP, fatty acid binding protein, NCX1, mammalian heart Na⁺/Ca²⁺ exchanger; NCXSQ1, squid nerve Na⁺/Ca²⁺ exchanger; MgATP, Magnesium adenosine 5' triphosphate; LBP, lipid-binding protein; CRBP, cellular retinol binding protein; H⁺_i, intracellular H⁺; Na⁺_i, intracellular Na⁺; Ca²⁺_i, intracellular Ca²⁺; PtdIns(4,5)P₂, phosphatidylinositol-4,5 biphosphate; NMG, N-methyl-D-glucamine; CHES, N-Cyclohexyl-2-aminoethanesulfonic acid; MOPS, 3-(N-morpholino)propanesulfonic acid; HRMS, high resolution mass spectrometry; ESI-MS, electrospray ionization mass spectrometry; LC-MS, liquid-chromatography coupled to mass spectrometry.

Dimerization properties of RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis

D. Bellini and M. Papiz

Structural basis for bathochromic shift of fluorescence in far-red fluorescent proteins eqFP650 and eqFP670

S. Pletnev, N. V. Pletneva, E. A. Souslova, D. M. Chudakov, S. Lukyanov, A. Wlodawer, Z. Dauter and V. Pletnev

Synopsis: Crystal structures of far-red fluorescent proteins eqFP650 and eqFP670 are solved at 1.8 Å and 1.6 Å resolution, respectively. This permitted identification of the structural elements responsible for bathochromic shift in both considered far-red FPs.

High resolution crystal structure of the isolated ribosomal L1 stalk

S. Tishchenko, A. Gabdulkhakov, N. Nevskaya, A. Sarskikh, O. Kostareva, E. Nikonova, A. Sycheva, S. Moshkovskii, M. Garber and S. Nikonov

X-ray structure of p38 bound to TAK-715: Comparison to three classic inhibitors

R. Azevedo, M. van Zeeland, H. Raaijmakers, B. Kazemier, J. de Vlieg and A. Oubrie

Synopsis: Presented is the first X-ray structure of p38 co-crystallized with TAK-715, as well as new high resolution structures of p38 bound to SB-203580, SCIO-469, and VX-745. The impact of crystallization conditions and selectivity profiles on protein conformation is discussed.

Structure features of single strand DNA(ssDNA) binding protein MoSub1 from Magnaporthe oryzae

J. Huang, Y. Zhao, D. Huang, H. Liu, N. Justin, W. Zhao, J. Liu and Y. Peng

Synopsis: The crystal structure of MoSub1, Sub1/PC4 ortholog from rice blast fungus, has two novel features in the N-terminal and C-terminal to the DNA binding domain. It has similar dimer interface and DNA binding region to PC4 and the protein binds single stranded DNA tightly.

Structural and biochemical characterization of a trapped coenzyme A adduct of C. elegans glucosamine-6-phosphate N-acetyltransferase

H. C. Dorfmueller, W. Fang, F. V. Rao, D. E. Blair, H. Attrill and D. M. F. van Aalten

Synopsis: Glucosamine-6-phosphate N-acetyltransferase is an essential enzyme of the eukaryotic UDP-GlcNAc biosynthetic pathway. A crystal structure at 1.55 Å resolution reveals a highly unusual covalent product complex and biochemical studies investigate the function of a fully conserved active site cysteine.

The promiscuous binding of the Fyn-SH3 domain to a peptide from the NS5A protein

J. M. Martin-Garcia, I. Luque, J. Ruiz-Sanz and A. Camara-Artigas

Synopsis: The promiscuous binding of a NS5A peptide to the Fyn-SH3 domain

Proline: Mother Nature's Cryoprotectant Applied to Protein Crystallography

T. A. Pemberton, B. R. Still, E. M. Christensen, H. Singh, D. Srivastava and J. J. Tanner

A universal indicator dye pH assay for crystallization solutions and other high-throughput applications

J. Newman, R. A. Sayle and V. J. Fazio

Synopsis: A rapid, plate-based pH assay has been developed that takes advantage of automation available in a protein crystallization laboratory.

The Use of Workflows in the Design and Implementation of Complex Experiments in Macromolecular Crystallography

S. Brockhauser, O. Svensson, M. W. Bowler, M. Nanao, E. Gordon, R. M. F. Leal, A. Popov, M. Gerring, A. A. McCarthy and A. Gotz

Synopsis: A powerful and easy to use workflow environment has been developed at the ESRF for combining experiment control with on-line data analysis on synchrotron beamlines. This tool opens the possibility of automating complex experiments without the need of expertise in instrumentation control and programming, but rather accessing defined beamline services.

RCrane: Semi-automated RNA model building

K. S. Keating and A. M. Pyle

Synopsis: RCrane is a new tool for the partially automated building of RNA crystallographic models into electron density maps of low or intermediate resolution. This tool helps crystallographers to place phosphates and bases into electron density, and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides.

Structure of the branched-chain aminotransferase from Streptococcus mutans

J. Ruan, J. Hu, A. Yin, W. Wu, X. Cong, X. Feng and S. Li

Synopsis: We report the crystal structure of the branched-chain aminotransferase from Streptococcus mutans to 1.9 Å resolution.

The -ray Structure of Salmonella typhimurium Uridine Phosphorylase Complexed with 5-Fluorouracil and Molecular Modeling of the Complex of 5-Fluorouracil with Uridine Phosphorylase from Vibrio cholerae

A. A. Lashkov, S. E. Sotnichenko, I. I. Prokofiev, A. G. Gabdulkhakov, I. I. Agapov, A. A. Shtill, C. Betzel, A. S. Mironov and A. M. Mikhailov

Synopsis: We report the X-ray structures and in silico models of complexes of the drug 5-fluorouracil (5-FURa) with uridine phosphorylases from Salmonella typhimurium (StUPh) and Vibrio cholerae (VchUPh).

The PAD region in the mycobacterial dinB homolog MsPolIV exhibits positional heterogeneity

A. Sharma, V. Subramanian and D. T. Nair

Significant reduction in errors associated with non-bonded contacts in protein crystal structures: Automated all-atom refinement with PrimeX

J. A. Bell, K. L. Ho and R. Farid

Synopsis: All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close non-bonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models better-suited for use in computational chemistry and related applications.

Structures of the gamma-class carbonic anhydrase homolog yrdA suggest a possible allosteric switch

H.-M. Park, J.-H. Park, J.-W. Choi, J. Lee, B. Y. Kim, C.-H. Jung and J.-S. Kim

Synopsis: The crystal structures of YrdA from E. coli show conformations that have not been reported in -CA family proteins.

Structural plasticity of tubulin assembly probed by Vinca domain ligands

F. M. Ranaivoson, B. Gigant, S. Berritt, M. Joullié and M. Knossow

Synopsis: The structure of ustiloxin D bound to tubulin was determined at a resolution which allows interatomic interactions to be defined and provides a basis for the structure-based design of ligands with improved activity. We also show how local interactions of Vinca domain ligands with tubulin influence relative positioning of the latter and lead to the large-scale polymorphism of ligand-mediated tubulin assemblies.

Crystallographic analysis of conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like folding

H. Chen, N. Shi, Y. Gao, X. Li, M. Teng and L. Niu

The structure of the catalytic core module from the Chaetomium thermophilum family GH6 cellobiohydrolase Cel6A

A. J. Thompson, T. Heu, T. Shaghasi, R. Benyam, A. Jones, E. P. Friis, K. S. Wilson and G. J. Davies

Synopsis: The three-dimensional structure of an industrially relevant cellulase in complex with ligands has been determined at a resolution of 1.9 Å.

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands - a tool to study the unique hinge region plasticity of the enzyme without packing bias

K. Klopffleisch, O.-G. Issinger and K. Niefind

Nanoliter Scale Crystallization Using Acoustic Liquid Transfer Technology

A. Villaseñor, A. Wong, A. Shao, A. Garg, T. J. Donohue, A. Kuglstatter and S. F. Harris

Synopsis: Acoustic droplet ejection achieves precise, tipless, non-invasive transfer of diverse aqueous solutions enabling nanoliter scale crystallization trials. The rapid, scalable technique demonstrated successful crystal growth with diverse targets in drop volumes as small as 20 nL.

An engineered PII protein variant sensing a novel ligand: atomic resolution structure of the complex with citrate

K. Zeth, O. Fokina and K. Forchhammer

The narrow active-site cleft of O-acetylserine sulfhydrylase from Leishmania donovani allows complex formation with serine acetyltransferases having a range of C-terminal sequences

I. Raj, S. Kumar and G. Samudrala

Synopsis: O-Acetylserine sulfhydrylase (OASS) from L. donovani can bind to serine acetyltransferase (SAT) C-terminal mimicking peptides having a range of bulkiness; the strength of these interactions correlates with the size of the peptide side chains and the size of the active-site cleft. Differences in interactions of OASS and SAT from various species may be explained by the size of the active-site cleft

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

T. C. Terwilliger, R. J. Read, P. D. Adams, A. T. Brunger, P. V. Afonine, R. W. Grosse-Kunstleve and L.-W. Hung

Low- and room-temperature X-ray structures of protein kinase A ternary complexes shed new light on its activity

A. Y. Kovalevsky, H. Johnson, B. L. Hanson, M. J. Waltman, S. Z. Fisher, S. Taylor and P. Langan

Synopsis: ATP bound in the active site of protein kinase A is readily hydrolysed to ADP and free phosphate by X-ray irradiation at room temperature. The phosphate ion observed in the active site causes a dramatic conformational change of the bound peptide inhibitor.

The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property

E. Hilario, Y. Li, D. Niks and L. Fan

Synopsis: The crystal structure of a putative general stress protein from the citrus canker bacterium X. citri pv. citri was determined to 2.5 Å resolution.

ATP forms a stable complex with the essential histidine kinase WalK (YycG) domain

R. Celikel, V. H. Veldore, I. Mathews, K. M. Devine and K. I. Varughese

A single mutation restores the binding activity of an adhesion-deficient family 3 carbohydrate-binding module

O. Yaniv, S. Petkun, L. J. W. Shimon, E. A. Bayer, R. Lamed and F. Frolow

Synopsis: Crystal structures of the family 3b carbohydrate-binding module (CBM3b) of the cellulosomal multimodular hydrolytic enzyme cellobiohydrolase 9A (Cbh9A) from C. thermocellum and of its mutant Cbh9A CBM3b^N126W have been determined at 2.20 and 1.04 Å resolution, respectively. This mutation restores the cellulose-binding properties of the adhesion-deficient CBM.

High-resolution structures of Neotermes koshunensis -glucosidase mutants provide insights into the catalytic mechanism and the synthesis of glucoconjugates

W.-Y. Jeng, N.-C. Wang, C.-T. Lin, W.-J. Chang, C.-I. Liu and A.H.-J. Wang

Protonation-state determination in proteins using high-resolution X-ray crystallography: effects of resolution and completeness

S. J. Fisher, M. P. Blakeley, M. Cianci, S. McSweeney and J. R. Helliwell

Synopsis: A bond-distance analysis to determine the protonation states of ionizable amino acids has been made for trypsin at 1.2 Å resolution, subtilisin at 1.26 Å resolution and lysozyme at 0.65 Å resolution. This was effective for Asp and Glu but not for His.

Outrunning free radicals in room-temperature macromolecular crystallography

R. L. Owen, D. Axford, J. E. Nettleship, R. J. Owens, J. I. Robinson, A. W. Morgan, A. S. Doré, G. Lebon, C. G. Tate, E. E. Fry, J. Ren, D. I. Stuart and G. Evans

Synopsis: A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector.

Structure of a post-translationally processed heterodimeric double-headed Kunitz-type serine protease inhibitor from potato

E. M. Meulenbroek, E. A. J. Thomassen, L. Pouvreau, J. P. Abrahams, H. Gruppen and N. S. Pannu

Synopsis: The structure of potato serine protease inhibitor, the most abundant protease inhibitor in potatoes, is reported and sheds light on the inhibition mechanism of this protein.

Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors

S. J. Lee, S.-J. Lee, S. K. Lee, H.-J. Yoon, H. H. Lee, K. K. Kim, B. J. Lee, B. I. Lee and S. W. Suh

Synopsis: Crystal structures of peptide deformylase from S. aureus in complex with novel inhibitors are presented together with their functional analysis. A detailed comparative analysis of these structures as well as the activities of the inhibitors allowed the elucidation of distinctive structural changes which depend upon the class of inhibitor.

Structures of Helicobacter pylori uridylate kinase: insight into release of the product UDP

C.-H. Chu, M.-H. Liu, P.-C. Chen, M.-H. Lin, Y.-C. Li, C.-D. Hsiao and Y.-J. Sun

Crystal structure and substrate specificity of the thermophilic serine:pyruvate aminotransferase from Sulfolobus solfataricus

C. Sayer, M. Bommer, M. Isupov, J. Ward and J. Littlechild

Synopsis: X-ray structures of S. solfataricus serine:pyruvate aminotransferase in different intermediate states and in complex with inhibitor have increased our understanding of the enzyme mechanism and have allowed an insight into the substrate specificity of this industrially important enzyme.

Biochemical and structural characterization of the GTP-preferring succinyl-CoA synthetase from Thermus aquaticus

M. A. Joyce, K. Hayakawa, W. T. Wolodko and M. E. Fraser

Synopsis: Succinyl-CoA synthetase catalyzes the reaction succinyl-CoA + NDP + P_i succinate + CoA + NTP, where N denotes adenosine or guanosine. The enzyme from T. aquaticus was characterized biochemically and its structure was determined in complex with GDP-Mn²⁺, the preferred nucleotide.

Structural basis of nuclear import of flap endonuclease 1 (FEN1)

A. C. de Barros, A. A. S. Takeda, C.-W. Chang, B. Kobe and M. R. M. Fontes

The structure of a GH10 xylanase from Fusarium oxysporum reveals the presence of an extended loop on top of the catalytic cleft

M. Dimarogona, E. Topakas, P. Christakopoulos and E. D. Chrysina

Synopsis: The structure of a xylanase from F. oxysporum (FoXyn10a) was determined at 1.94 Å resolution. FoXyn10a adopts the (/)₈-barrel fold of the GH10 family, with an extended loop above the catalytic site with potential implications for enzymatic function.

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