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 29 January 2015

Structure and catalytic mechanism of the evolutionarily unique bacterial chalcone isomerase

M. Thomsen, A. Tuukkanen, J. Dickerhoff, G. J. Palm, H. Kratzat, D. I. Svergun, K. Weisz, U. T. Bornscheuer and W. Hinrichs

Synopsis: Elucidation of the first bacterial chalcone isomerase of native and substrate bound crystal structures reveals structural homology to the chlorite dismutase, but no structural relation to the plant chalcone isomerase suggesting a different evolutionary history. The catalytic site of the bacterial isomerase depends on a histidine sidechain, in contrast to the catalytic water molecule of the plant enzyme.


Accepted 28 January 2015

Structural and biophysical characterization of epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization

J. L. Johnson, K. C. Entzminger, J. Hyun, S. Kalyoncu, D. P. Heaner, I. A. Morales, A. Sheppard, J. C. Gumbart, J. A. Maynard and R. L. Lieberman

Synopsis: Fab fragment with nanomolar affinity for the peptide sequence EYMPME was engineered and characterized by structural, biophysical, and computational methods for its potential use as a membrane protein crystallization chaperone.


Accepted 27 January 2015

Crystal structure of Microcystis aeruginosa microcystin synthetase McyG adenylation-peptidyl carrier didomain

X.-F. Tan, Y.-N. Dai, K. Zhou, Y.-L. Jiang, Y.-M. Ren, Y. Chen and C.-Z. Zhou

Synopsis: Provided is the first structure of A-PCP didomain in which A domain is in adenylated state complexed with the intermediate L-Phe-AMP.


Accepted 25 January 2015

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

A. E. Langkilde, K. L. Morris, L. C. Serpell, D. I. Svergun and B. Vestergaard

Synopsis: The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition as the prevailing mechanism of elongation and a model of the peptide packing in the fibrils is obtained.


Accepted 25 January 2015

Covalent adduct of MbtN, an acyl-ACP de­hydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket

A.-F. Chai, E. M. M. Bulloch, G. L. Evans, J. S. Lott, E. N. Baker and J. M. Johnston

Synopsis: The structure of the MbtN (Rv1346), presented here, supports its annotation as the double bond forming dehydrogenase involved in the biosynthesis of mycobactin T in Mycobacterium tuberculosis and reveals a novel FAD-PEG covalent adduct bound in a unique acyl-binding cavity.


Accepted 23 January 2015

Elucidation of crystal structure of Coriolopsis caperata laccase: restoration of the structure and activity of native enzyme from T2 depleted form by copper ions

O. A. Glazunova, K. M. Polyakov, T. V. Fedorova, P. V. Dorovatovsky and O. V. Koroleva


Accepted 22 January 2015

Structure of the N-terminal domain of the protein Expansion: an 'Expansion' to the Smad MH2 fold

M. Beich-Frandsen, E. Aragón, M. Llimargas, J. Benach, A. Riera, J. Pous and M. J. Macias

Synopsis: Expansion is a modular protein conserved in Protostomes. We have determined the first structure of the N-terminal domain of Expansion, at 1.6 Å resolution. The new domain (N[alpha]-MH2) shares with the Smads the main characteristics of the MH2 fold but contains an extra helix (N[alpha]), which lies across the domain, covering one side of the beta-sandwich. Few structural differences between the canonical MH2 domain and that of the Expansion N[alpha]-MH2 seem to preclude its participation in TGF-[beta] signaling. The new N[alpha]-MH2 domain belongs to the Smad/FHA superfamily of structures.


Accepted 21 January 2015

ANS complex of St John's wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning

J. Sliwiak, Z. Dauter, M. Kowiel, A. J. McCoy, R. J. Read and M. Jaskolski

Synopsis: Hyp-1, a pathogenesis-related class 10 (PR-10) protein from Hypericum perforatum, was crystallized in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS). The asymmetric unit of the tetartohedrally twinned crystal contains 28 copies of the protein arranged in columns with non-crystallographic sevenfold translational symmetry, and with additional pseudotetragonal rotational NCS.


Accepted 21 January 2015

Novel crystalline phase and first order phase transitions of human insulin complexed with two distinct phenol-derivatives

A. Valmas, K. Magiouf, S. Fili, M. Norrman, G. Schluckebier, D. Beckers, T. Degen, J. Wright, A. Fitch, F. Gozzo, A. E. Giannopoulou, F. Karavassili and I. Margiolaki


Accepted 20 January 2015

Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

Z. Wang, Z. Qiao, S. Ye and R. Zhang


Accepted 20 January 2015

The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

Z. Yurtsever, S. M. Scheaffer, A. D. Romero, M. J. Holtzman and T. J. Brett


Accepted 20 January 2015

Structure of Arabidopsis thaliana Rubisco activase

D. Hasse, A. M. Larsson and I. Andersson

Synopsis: The crystal structure of Rubisco activase from Arabidopsis thaliana is presented. The structure shows a high degree of conformational flexibility and indicates that subtle structural differences may influence interactions in the oligomeric complexes of green-type Rubisco activases.


Accepted 20 January 2015

Structure of stru­thiocalcin-1, an intramineral protein from Stru­thio camelus eggshell, in two crystal forms

R. R. Ruiz-Arellano, F. J. Medrano, A. Moreno and A. Romero

Synopsis: The crystal structure of Struthiocalcin-1 (SCA-1) from ostrich eggshell has been determined in two different crystal forms at 1.50 Å, displaying the characteristic C-type lectin-like fold with a surface decorated with acidic residues, highlighting the overall negative charge in SCA-1.


Accepted 19 January 2015

Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa

J. W. Schmidberger, R. Schnell and G. Schneider


Accepted 17 January 2015

Radiation decay of thaumatin crystals at three X-ray energies

D. Liebschner, G. Rosenbaum, M. Dauter and Z. Dauter

Synopsis: A series of diffraction images of thaumatin crystals at identical small, 2° rotation intervals were recorded at three different X-ray energies (6.33 keV, 12.66 keV and 19.0 keV), using five crystals at each energy. The decay of average diffraction intensities at 100 K due to radiation damage was analyzed and the dose that diminishes reflection intensities to 70% was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.


Accepted 16 January 2015

Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein

P. Szewczyk, H. Tao, A. P. McGrath, M. Villaluz, S. D. Rees, S. C. Lee, R. Doshi, I. L. Urbatsch, Q. Zhang and G. Chang

Synopsis: Co-crystal structures of P-glycoprotein with a series of engineered ligands reveal multiple ligand binding modes, a ligand-binding site on the outer surface of the transporter and a conformational change that may couple to ATP hydrolysis.


Accepted 16 January 2015

A noncanonical PWI domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein

E. Absmeier, L. Rosenberger, L. Apelt, C. Becke, K. F. Santos, U. Stelzl and M. C. Wahl

Synopsis: Crystal structure and biochemical analyses reveal the presence of a PWI-like domain in the N-terminal helicase-associated region of the spliceosomal Brr2 protein, which does not stably bind nucleic acids but instead constitutes part of a protein-protein interaction region that binds several spliceosomal proteins in a yeast 2-hybrid assay.


Accepted 15 January 2015

The rate of cis-trans conformation errors is increasing in low-resolution crystal structures

T. I. Croll

Synopsis: The growing profusion of spurious non-proline cis peptide bonds in deposited structures suggests that a report on these should be added to standard structural quality checks.


Accepted 12 January 2015

The structure of the hexameric atrazine chloro­hydrolase AtzA

T. S. Peat, J. Newman, S. Balotra, D. Lucent, A. C. Warden and C. Scott

Synopsis: The structure of atrazine chlorohydrolase (AtzA) is presented and used to reinterpret data from genetic, biochemical and evolutionary studies, providing insight into why this recently evolved enzyme appears to be poorly adapted for its physiological substrate compared with the alternative metal-dependent atrazine decholorinase, TrzN.


Accepted 9 January 2015

Structure of N-myristoyl transferase from Aspergillus fumigatus

T. Shimada, M. Suzuki and S.- Katakura


Accepted 8 January 2015

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

G. Chojnowski, T. Walen, P. Piatkowski, W. Potrzebowski and J. M. Bujnicki


Accepted 7 January 2015

High-pressure protein crystallography of hen egg-white lysozyme

H. Yamada, T. Nagae and N. Watanabe

Synopsis: The crystal structure of hen egg-white lysozyme (HEWL) was analyzed under pressures of up to 950 MPa. The high pressure modified the conformation of the molecule and induced a novel phase transition in the tetragonal crystal of HEWL.


Accepted 6 January 2015

NuProPlot: nucleic acid and protein interaction-analysis and plotting program

L. Pradhan and H.-J. Nam

Synopsis: NuProPlot is a web-based automatic analysis and two-dimensional schematization program for protein-nucleic acid complexes. It can handle any type of nucleic acid ranging from a few base pairs of simple DNA to thousands of RNA bases in complex protein-RNA structures with user-friendly interactive options.


Accepted 6 January 2015

Structure of Csd3 from Helicobacter pylori, a cell shape-determining metallopeptidase

D. R. An, H. S. Kim, J. Kim, H. N. Im, H. J. Yoon, J. Y. Yoon, J. Y. Jang, D. Hesek, M. Lee, S. Mobashery, S.-J. Kim, B. I. Lee and S. W. Suh

Synopsis: H. pylori Csd3 (HP0506), together with other peptidoglycan hydrolases, plays an important role in determining cell shape. Its crystal structure in the latent state is reported.


Accepted 30 December 2014

Automated de novo phasing and model building of coiled-coil proteins

S. Rämisch, R. Lizatovic and I. André

Synopsis: A fully automated procedure is presented that finds molecular-replacement solutions for coiled-coil structures based on models from de novo structure prediction.


Accepted 25 December 2014

FEM: feature-enhanced map

P. V. Afonine, N. W. Moriarty, M. Mustyakimov, O. V. Sobolev, T. C. Terwilliger, D. Turk, A. Urzhumtsev and P. D. Adams


Accepted 23 December 2014

Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6

A. Bujacz, M. Rutkiewicz-Krotewicz, K. Nowakowska-Sapota and M. Turkiewicz

Synopsis: Two crystal structures of an aminotransferase from Psychrobacter sp. B6 have been determined at resolutions of 2.19 Å (native enzyme) and 2.76 Å (complex with aspartate). The protein was expressed in E. coli and specific activity tests indicated that aromatic amino acids and aspartate are the substrates.


Accepted 22 December 2014

Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states

T. Skálová, J. Bláha, K. Harlos, J. Dusková, T. Koval, J. Stránský, J. Hasek, O. Vanek and J. Dohnálek

Synopsis: Four crystal structures of human LLT1, a ligand for human NKR-P1, are reported.


Accepted 22 December 2014

An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

J. E. M. M. Wong, S. R. Midtgaard, K. Gysel, M. B. Thygesen, K. K. Sørensen, K. J. Jensen, J. Stougaard, S. Thirup and M. Blaise

Synopsis: The crystal and solution structures of the T. thermophilus NlpC/P60 D,L-endopeptidase as well as the co-crystal structure of its N-terminal LysM domains bound to chitohexaose allow a proposal to be made regarding how the enzyme recognizes peptidoglycan.


Accepted 19 December 2014

Structure of a highly acidic [beta]-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs+-selective binding site

S. Arai, Y. Yonezawa, N. Okazaki, F. Matsumoto, C. Shibazaki, R. Shimizu, M. Yamada, M. Adachi, T. Tamada, M. Kawamoto, H. Tokunaga, M. Ishibashi, M. Blaber, M. Tokunaga and R. Kuroki

Synopsis: The tertiary structure of a [beta]-lactamase derived from the halobacterium Chromohalobacter sp. 560 (HaBLA) was determined by X-ray crystallography. Three unique Sr2+-binding sites and one Cs+-binding site were discovered in the HaBLA molecule.


Accepted 19 December 2014

Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

M. E. Ivanova, G. C. Fletcher, N. O'Reilly, A. G. Purkiss, B. J. Thompson and N. Q. McDonald

Synopsis: This study characterizes the interaction between the carboxy-terminal (ERLI) motif of the essential polarity protein Crb and the Pals1/Stardust PDZ-domain protein. Structures of human Pals1 PDZ with and without a Crb peptide are described, explaining the highly conserved nature of the ERLI motif and revealing a sterically blocked peptide-binding groove in the absence of ligand.


Accepted 19 December 2014

Structures of three polycystic kidney disease-like domains from Clostridium histolyticum collagenases ColG and ColH

R. Bauer, K. Janowska, K. Taylor, B. Jordan, S. Gann, T. Janowski, E. C. Latimer, O. Matsushita and J. Sakon

Synopsis: The surface properties and dynamics of PKD-like domains from ColG and ColH differ.


Accepted 18 December 2014

Automating the application of smart materials for protein crystallization

S. Khurshid, L. Govada, H. F. El-Sharif, S. M. Reddy and N. E. Chayen


Accepted 17 December 2014

A di­sulfide-bond cascade mechanism for arsenic(III) S-adenosylme­thionine methyltransferase

K. Marapakala, C. Packianathan, A. A. Ajees, D. S. Dheeman, B. Sankaran, P. Kandavelu and B. P. Rosen

Synopsis: Two of the four conserved cysteine residues of an arsenic(III) S-adenosylmethionine methyltransferase bind aromatic arsenicals. The other two conserved cysteine residues form a disulfide bond.


Accepted 17 December 2014

The mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP

C.-F. Zhu, W. Wei, X. Peng, Y.-H. Dong, Y. Gong and X.-F. Yu

Synopsis: Crystal structures of a GTP-bound SAMHD1 dimer and GTP/dNTP-bound SAMHD1 tetramers elucidate the mechanism of substrate-controlled allosteric regulation of SAMHD1 activated by GTP.


Accepted 17 December 2014

The 1.65 Å resolution structure of the complex of AZD4547 with the kinase domain of FGFR1 displays exquisite molecular recognition

Y. Yosaatmadja, A. V. Patterson, J. B. Smaill and C. J. Squire

Synopsis: The complex between AZD4547 and the kinase domain of FGFR1 displays exquisite molecular recognition between ligand and protein, with the formation of an extended cavity by the closure of the P-loop.


Accepted 10 December 2014

Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes

S. O. Dahms, M. C. Mayer, D. Roeser, G. Multhaup and M. E. Than

Synopsis: Two X-ray structures of APLP1 E2 with and without a heparin dodecasaccharide are presented, revealing two distinct binding modes of the protein to heparan sulfate. The data provide a mechanistic explanation of how APP-like proteins bind to heparan sulfates and how they specifically recognize nonreducing structures of heparan sulfates.


Accepted 9 December 2014

Three-dimensional structures of Plasmodium falciparum spermidine synthase with bound inhibitors suggest new strategies for drug design

J. Sprenger, B. Svensson, J. Hålander, J. Carey, L. Persson and S. Al-Karadaghi


Accepted 8 December 2014

Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s

J. Song, S. Kose, A. Watanabe, S.-Y. Son, S. Choi, H. Hong, E. Yamashita, I. Y. Park, N. Imamoto and S. J. Lee

Synopsis: The crystal structure and functions of Hikeshi, a nuclear transport receptor of Hsp70s, are described.


Accepted 5 December 2014

Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylamino­acyl peptidase and their implications for functionality

D. K. Menyhárd, Z. Orgován, Z. Szeltner, I. Szamosi and V. Harmat

Synopsis: A mechanism for the dual function of oligopeptidases involves decoupling substrate binding and catalytic activity. Crystal structures of the A. pernix acylaminoacyl peptidase-covalent inhibitor complex provide insights into the role of substrates in this mechanism.


Accepted 4 December 2014

Genuine open form of the pentameric ligand-gated ion channel GLIC

Z. Fourati, L. Sauguet and M. Delarue


Accepted 4 December 2014

The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity

U. Fischer, S. Hertlein and C. Grimm

Synopsis: The crystal structure of apo ArnA features an unexpected central binding pocket and explains the strong cooperative effect observed in the dehydrogenase activity of ArnA.


Accepted 4 December 2014

X-ray, spectroscopic and normal-mode dynamics of calexcitin: structure-function studies of a neuronal calcium-signalling protein

P. T. Erskine, A. Fokas, C. Muriithi, H. Rehman, L. A. Yates, A. Bowyer, I. S. Findlow, R. Hagan, J. M. Werner, A. J. Miles, B. A. Wallace, S. A. Wells, S. P. Wood and J. B. Cooper


Accepted 3 December 2014

Structural insights into Aspergillus fumigatus lectin specificity: AFL binding sites are functionally non-equivalent

J. Houser, J. Komarek, G. Cioci, A. Varrot, A. Imberty and M. Wimmerova

Synopsis: The interaction between the A. fumigatus lectin AFL and biologically relevant oligosaccharides has been examined. The functional data were combined with detailed structures of the protein-saccharide complexes to understand the ligand binding at the atomic level.


Accepted 1 December 2014

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

J. Ruan, T. Mouveaux, S. H. Light, G. Minasov, W. F. Anderson, S. Tomavo and H. M. Ngô

Synopsis: The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites.


Accepted 15 November 2014

Crystallization of lysozyme with (R)-, (S)- and (RS)-2-methyl-2,4-pentanediol

M. Stauber, J. Jakoncic, J. Berger, J. M. Karp, A. Axelbaum, D. Sastow, S. V. Buldyrev, B. J. Hrnjez and N. Asherie

Synopsis: Crystallization of lysozyme with (R)-2-methyl-2,4-pentanediol produces more ordered crystals and a higher resolution protein structure than crystallization with (S)-2-methyl-2,4-pentanediol. The results suggest that chiral interactions with chiral additives are important in protein crystal formation.




































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