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.

Structural characteristics of alkaline phosphatase from the moderately halophilic bacterium Halomonas sp. 593

S. Arai, Y. Yonezawa, M. Ishibashi, F. Matsumoto, M. Adachi, T. Tamada, H. Tokunaga, M. Blaber, M. Tokunaga and R. Kuroki

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.

Structure of Rv2372c identifies a RsmE-like methyltransferase from M. tuberculosis

A. Kumar, S. Kumar and B. Taneja

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.

Identification of a novel polyfluorinated compound as a lead to inhibit human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design

A. Cousido-Siah, F. X. Ruiz, A. Mitschler, S. Porté, Á. R. de Lera, M. J. Martín, S. Manzanaro, J. A. de la Fuente, F. Terwesten, M. Betz, G. Klebe, J. Farrés, X. Parés and A. Podjarny

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.

Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal a metal-independent catalysis and inhibitor binding

K.-F. Huang, H.-L. Hsu, S. Karim and A.H.-J. Wang

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.

Structural insights into a novel ARM repeat protein CTNNBL1 and its association with the hPrp19/CDC5L complex

J.-W. Ahn, S. Kim, E.-J. Kim, Y.-J. Kim and K.-J. Kim

Structural and thermodynamic basis of the inhibition of Leishmania major Farnesyl Diphosphate Synthase by nitrogen containing bisphosphonates

S. Aripirala, D. Gonzalez-Pacanowska, E. Oldfield, M. Kaiser, L. M. Amzel and S. B. Gabelli

Synopsis: Structural insights of Leishmania major Farnesyl diphosphate synthase, a key enzyme in the mevalonate pathway.

New insights into the catalytic active site structure of multicopper oxidase

H. Komori, R. Sugiyama, K. Kataoka, K. Miyazaki, Y. Higuchi and T. Sakurai

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.

Crystal structure of authentic spore photoproduct lesion in DNA suggests basis for recognition

I. Singh, Y. Lian, L. Li and M. M. Georgiadis

Synopsis: The structure of a spore photoproduct lesion in duplex DNA is described.

Structure of the Extended-Spectrum Class C -Lactamase ADC-1 from Acinetobacter baumannii

M. Bhattacharya, M. Toth, N. T. Antunes, C. A. Smith and S. B. Vakulenko

Synopsis: The crystal structure of the class C extended-spectrum cepahalosporinase ADC-1 has been solved to 1.2 Å resolution.

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution

N. Azim, E. Deery, M. J. Warren, B. A. A. Wolfenden, P. Erskine, J. B. Cooper, A. Coker, S. P. Wood and M. Akhtar

Synopsis: The enzyme porphobilinogen deaminase (PBGD) (hydroxymethylbilane synthase; EC 2.5.1.61) 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.

Notes of a protein crystallographer: the beauty of rose windows and the different meanings of symmetry

C. Abad-Zapatero

Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

F. Forneris, B. T. Burnley and P. Gros

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.

Role of light chain constant domain switch in the structure and functionality of A17 reactibody

N. Ponomarenko, S. D. Chatziefthimiou, I. Kurkova, Y. Mokrushina, A. Stepanova, I. Smirnov, M. Avakyan, T. Bobik, A. Mamedov, V. Mitkevich, A. Belogurov, O. Fedorova, M. Dubina, A. Golovin, V. Lamzin, A. Friboulet, A. Makarov, M. Wilmanns and A. Gabibov

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.

Structures of the Ca²⁺-regulated photoprotein obelin Y138F mutant before and after bioluminescence support a catalytic function of a water molecule in the reaction

P. V. Natashin, W. Ding, E. V. Eremeeva, S. V. Markova, J. Lee, E. S. Vysotski and Z.-J. Liu

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.

Exploiting large non-isomorphous differences for phase determination of a G-segment invertase-DNA complex

C. J. Ritacco, T. A. Steitz and J. Wang

Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor

T. Kim, T. Duong, C.- Wu, J. Choi, N. Lan, S. W. Kang, N. K. Lokanath, D.-W. Shin, H.-Y. Hwang and K. K. Kim

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.

Structural analysis of -glucosidase mutants derived from a hyperthermophilic tetrameric structure

M. Nakabayashi, M. Kataoka, Y. Mishima, Y. Maeno and K. Ishikawa

Synopsis: Substitutive mutations that convert a tetrameric -glucosidase into a dimeric state lead to improve its crystal-quality.

Conformational transitions in the subunit of the archaeal translation initiation factor 2

O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov and M. Garber

Structure of proteolytically resistant analog of [NLys]⁵SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease mediated proteolysis

S. Krzywda, M. Jaskolski, K. Rolka and M. J. Stawikowski

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.

Crystal structures of substrate-bound chitinase from the psychrophilic bacterium Moritella marina and its structure in solution

P. H. Malecki, C. E. Vorgias, M. V. Petoukhov, D. I. Svergun and W. Rypniewski

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.

Improving chances of successful protein structure determination with Random Forest classifier

S. Jahandideh, L. Jaroszewski and A. Godzik

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.

Crystal structure and conformational flexibility of the unligated FK506-binding protein FKBP12.6

H. Chen, S. M. Mustafi, D. M. LeMaster, Z. Li, A. Héroux, H. Li and G. Hernández

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.

Promoting Protein Crystallization Using a Plate with Simple Geometry

R.-Q. Chen, D.-C. Yin, Y.-M. Liu, Q.-Q. Lu, J. He and Y. Liu

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.

How precise are reported protein coordinate data?

Konagurthu, Allison, Abramson, Stuckey and Lesk

Synopsis: Information theory is used to estimate the precision of reported protein coordinates in the PDB.

PLP undergoes conformational changes during the course of an enzymatic reaction

H.-P.-T. Ngo, N. S. Cerqueira, J.-K. Kim, M.-K. Hong, P. A. Fernandes, M. J. Ramos and L.-W. Kang

Structure of Bacillus subtilis -glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site directed glutamate analogue

T. Ida, H. Suzuki, K. Fukuyama, J. Hiratake and K. Wada

Synopsis: Binding modes of acivicin, a classical and an electrophilic active-site directed glutamate analogue, to bacterial -glutamyltranspeptidases were diverse.

Nitrate in the active site of PTP1B is a putative mimetic of the transition state

P. W. Kenny, J. Newman and T. S. Peat

Structural basis for catalysis and ubiquitin recognition by the severe acute respiratory syndrome coronavirus papain-like protease

C.-Y. Chou, H.-Y. Lai, H.-Y. Chen, S.-C. Cheng, K.-W. Cheng and Y.-W. Chou

Synopsis: Crystal structure of the PL^pro C112S mutant in complex with Ub offers insight into the molecular basis of the PL^pro catalytic mechanism and its substrate binding. An N-cyclohexyl-2-aminethanesulfonic acid in the active site suggests a possible inhibiting approach.

Structures of AzrA and of AzrC complexed with substrate or inhibitor: insight into substrate specificity and catalytic mechanism

J. Yu, D. Ogata, Z. Gai, S. Taguchi, I. Tanaka, T. Ooi and M. Yao

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.

Structural and functional characterization of an Isd-type haem-degradation enzyme from Listeria monocytogenes

T. Duong, K. Park, T. Kim, S. W. Kang, M. J. Hanh, H.-Y. Hwang and K. K. Kim

Adherence to Bürgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes

S. H. Light, G. Minasov, M.-E. Duban and W. F. Anderson

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.

Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor

C. Zeymer, T. R. M. Barends, N. D. Werbeck, I. Schlichting and J. Reinstein

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.

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

P. Pachl, M. Fábry, I. Rosenberg, O. Simák, P. Rezácová and J. Brynda

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.

Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartrohedal twinning and sevenfold translational noncrystallographic symmetry

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

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.

Crystal structure and CRISPR RNA-binding site of the Cmr1 subunit of the Cmr interference complex

J. Sun, J.-H. Jeon, M. Shin, H.-C. Shin, B.-H. Oh and J.-S. Kim

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.

Structure of an unusual S-adenosylmethionine synthetase from Campylobacter jejuni

S. P. Zano, A. G. Pavlovsky and R. E. Viola

Identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex

J. L. Andersen, T. J. Schrøder, S. Christensen, D. Strandbygård, L. T. Pallesen, M. M. García-Alai, S. Lindberg, M. Langgård, J. C. Eskildsen, L. David, L. Tagmose, K. B. Simonsen, P. J. Maltas, L. C. B. Rønn, I. E. M. de Jong, I. J. Malik, J. Egebjerg, J.-J. Karlsson, S. Uppalanchi, D. R. Sakumudi, P. Eradi, S. P. Watson and S. Thirup

Synopsis: The identification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex are reported.

Ligand placement based on prior structures: the guided ligand-replacement method

H. E. Klei, N. W. Moriarty, N. Echols, T. C. Terwilliger, E. T. Baldwin, M. Pokross, S. Posy and P. D. Adams

The family-wide structure and function of human dual-specificity protein phosphatases

D. G. Jeong, C. H. Wei, B. Ku, T. J. Jeon, P. N. Chien, J. K. Kim, S. Y. Park, H. S. Hwang, S. Y. Ryu, H. S. Park, D. S. Kim, S. J. Kim and S. E. Ryu

Structure of the N-terminal domain of the effector protein LegC3 from Legionella pneumophila

D. Yao, M. Cherney and M. Cygler

Experiences with making diffraction image data available: What metadata do we need to archive?

L. M. J. Kroon-Batenburg and J. R. Helliwell

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.

Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant

P. Munshi, E. H. Snell, M. J. van der Woerd, R. A. Judge, D. A. A. Myles, Z. Ren and F. Meilleur

Fine-structural variance of family 3 carbohydrate-binding modules as extracellular biomass-sensing components of Clostridium thermocellum anti-^I factors

O. Yaniv, G. Fichman, I. Borovok, Y. Shoham, E. A. Bayer, R. Lamed, L. J. W. Shimon and F. Frolow

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.

Structure of choline oxidase in complex with the reaction product glycine betaine

F. Salvi, Y.-F. Wang, I. T. Weber and G. Gadda

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.

Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

Y. He, C. Roth, J. P. Turkenburg and G. J. Davies

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.

Factors correlating with significant differences between X-ray structures of myoglobin

A. A. Rashin, M. J. Domagalski, M. T. Zimmermann, W. Minor, M. Chruszcz and R. L Jernigan

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.

The crystal structure and biochemical characterization of Kif15: a bifunctional molecular motor involved in bipolar spindle formation and neuronal development

M. Klejnot, A. Falnikar, V. Ulaganathan, R. A. Cross, P. W. Baas and F. Kozielski

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.

Kinase crystal identification and ATP-competitive inhibitor screening using the fluorescent ligand SKF86002

L. J. Parker, S. Taruya, K. Tsuganezawa, N. Ogawa, J. Mikuni, K. Honda, Y. Tomabechi, N. Handa, M. Shirouzu, S. Yokoyama and A. Tanaka

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.

Small-angle scattering gives direct structural information about a membrane protein inside a lipid environment

S. A. R. Kynde, N. Skar-Gislinge, M. C. Pedersen, S. R. Midtgaard, J. B. Simonsen, R. Schweins, K. Mortensen and L. Arleth

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.

Structural and enzymatic characterization of a host-specificity determinant from Salmonella

A. C. Kohler, S. Spanò, J. E. Galán and C. E. Stebbins

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.

A unique octameric structure of Axe2, an intracellular acetyl-xylooligosaccharide esterase from Geobacillus stearothermophilus

S. Lansky, O. Alalouf, V. Solomon, A. Alhassid, L. Govada, N. E. Chayen, H. Belrhali, Y. Shoham and G. Shoham

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.

A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex

I. Russo Krauss, G. Parkinson, A. Merlino, C. A. Mattia, A. Randazzo, E. Novellino, L. Mazzarella and F. Sica

Novel complex MAD phasing and RNase H structural insights using selenium oligonucleotides

R. Abdur, O. O. Gerlits, J. Gan, J. Jiang, J. Salon, A. Y. Kovalevsky, A. A. Chumanevich, I. T. Weber and Z. Huang

Atomic resolution view into the structure-function relationships of the human myelin peripheral membrane protein P2

S. Ruskamo, R. P. Yadav, S. Sharma, M. Lehtimäki, S. Laulumaa, S. Aggarwal, M. Simons, J. Bürck, A. S. Ulrich, A. H. Juffer, I. Kursula and P. Kursula

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.

The structures of the kinase domain and UBA domain of MPK38 suggest the activation mechanism for kinase activity

Y.-S. Cho, J. Yoo, S. Park and H.-S. Cho

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.

The multiple nucleotide-divalent cation binding modes of Saccharomyces cerevisiae CK2 indicate a possible co-substrate hydrolysis product (ADP/GDP) release pathway

H. Liu, H. Wang, M. Teng and X. Li

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.

Structural analysis of the endogenous glycoallergen Hev b 2 (endo--1,3-glucanase) from Hevea brasiliensis and its recognition by human basophils

A. Rodríguez-Romero, A. Hernández-Santoyo, D. Fuentes-Silva, L. A. Palomares, S. Muñoz-Cruz, L. Yépez-Mulia and S. Orozco-Martínez

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.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography

A. Bhardwaj, S. R. Casjens and G. Cingolani

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.

Stealth carriers for low-resolution structure determination of membrane proteins in solution

S. Maric, N. Skar-Gislinge, S. Midtgaard, M. Thygesen, J. Schiller, H. Frielinghaus, M. Moulin, M. Haertlein, V. T. Forsyth, T. Günther-Pomorski and L. Arleth

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.

Automating crystallographic structure solution and refinement of protein-ligand complexes

N. Echols, N. W. Moriarty, H. E. Klei, P. V. Afonine, G. Bunkóczi, J. J. Headd, A. J. McCoy, R. D. Oeffner, R. J. Read, T. C. Terwilliger and P. D. Adams

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.

Structure of the full-length yeast Arp7-Arp9 heterodimer

J. Lobsiger, Y. Hunziker and T. J. Richmond

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.

High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies

V. Rimsa, T. C. Eadsforth, R. P. Joosten and W. N. Hunter

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.

Crystallographic study of FABP5 as an intracellular endocannabinoid transporter

B. Sanson, T. Wang, J. Sun, L. Wang, M. Kaczocha, I. Ojima, D. Deutsch and H. Li

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.

Structural basis for DNA recognition and nuclease processing by the Mre11 homologue SbcD in double-strand break repair

S. Liu, L. Tian, Y. Liu, X. An, Q. Tang, X. Yan and D. Liang

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.

Weak data do not make a free lunch, but only a cheap meal

Z. Luo, K. Rajashankar and Z. Dauter

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.

Structural enzymology of Helicobacter pylori methylthioadenosine nucleosidase in the futalosine pathway

R. Q. Kim, W. A. Offen, G. J. Davies and K. A. Stubbs

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.

Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart

S. Fieulaine, M. Desmadril, T. Meinnel and C. Giglione

A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8

S. Wang, M. Ogata, S. Horita, J. Ohtsuka, K. Nagata and M. Tanokura

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.

Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31

M. Lahoda, J. R. Mesters, A. Stsiapanava, R. Chaloupkova, M. Kuty, J. Damborsky and I. Kuta Smatanova

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.

Structural basis for DNA-mediated allosteric regulation facilitated by the AAA⁺ module of Lon protease

A.Y.-L. Lee, Y.-D. Chen, Y.-Y. Chang, Y.-C. Lin, C.-F. Chang, S.-J. Huang, S.-H. Wu and C.-H. Hsu

Structural insights into the catalytic mechanism of human squalene synthase

C.-I. Liu, W.-Y. Jeng, W.-J. Chang, M.-F. Shih, T.-P. Ko and A.H.-J. Wang

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.

Structure of the FP domain of Fbxo7 reveals a novel mode of protein-protein interaction

J. Shang, G. Wang, Y. Yang, X. Huang and Z. Du

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.

Breaking the indexing ambiguity in serial crystallography

W. Brehm and K. Diederichs

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.

Atomic resolution crystal structure of glutaredoxin 1 from Plasmodium falciparum and comparison with other glutaredoxins

M. Yogavel, T. Tripathi, A. Gupta, M. M. Banday, S. Rahlfs, K. Becker, H. Belrhali and A. Sharma

Synopsis: The structure of glutaredoxin 1 from P. falciparum has been determined at atomic resolution and its unique structural features have been dissected.

Structural characterization of new deoxycytidine kinase inhibitors rationalizes the affinity-determining moieties of the molecules

J. Nomme, J. M. Murphy, Y. Su, N. D. Sansone, A. L. Armijo, S. T. Olson, C. Radu and A. Lavie

Doing the right things

M. Jaskolski

Synopsis: Letter to the editor.

Structural basis for the broad specificity of a new family of amino-acid racemases

A. Espaillat, C. Carrasco-Lopez, N. Bernardo-Garcia, N. Pietrosemoli, L. H. Otero, L. Alvarez, M. A. de Pedro, F. Pazos, B. M. Davis, M. K. Waldor, J. A. Hermoso and F. Cava

The rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP

S. Pletnev, F. V. Subach, V. V. Verkhusha and Z. Dauter

Synopsis: An analysis of the rotational order-disorder structure of the reversibly photoswitchable red fluorescent protein rsTagRFP is presented.

Structure and mechanism of a type III secretion protease, NleC

W. Li, Y. Liu, X. Sheng, P. Yin, F. Hu, Y. Liu, C. Chen, Q. Li, C. Yan and J. Wang

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.

Crystallographic snapshots of initial steps in the collapse of the calmodulin central helix

P. Kursula

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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