Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 12 (December 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The phytohormone cytokinin (spheres) is bound in the cavity of a plant PR-10 protein upon its dimerization (gold and blue), in a process that starts plant-microbe symbiosis (p. 2365).

scientific comment


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [RE]  [Open access]

Acta Cryst. (2013). D69, 2293-2295  [ doi:10.1107/S0907444913024621 ]

Timely deposition of macromolecular structures is necessary for peer review

R. P. Joosten, H. Soueidan, L. F. A. Wessels and A. Perrakis

Synopsis: Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB.

Online 19 November 2013


letters to the editor


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2296  [ doi:10.1107/S0907444913029168 ]

Comment on Timely deposition of macromolecular structures is necessary for peer review by Joosten et al. (2013)

H. Berman, G. J. Kleywegt, H. Nakamura and J. L. Markley

Synopsis: A response to the article by Joosten et al. [(2013), Acta Cryst. D69, 2293-2295].

Online 19 November 2013


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2297  [ doi:10.1107/S090744491302917X ]

Comment on On the propagation of errors by Jaskolski (2013)

H. Berman, G. J. Kleywegt, H. Nakamura and J. L. Markley

Synopsis: A response to the article by Jaskolski [(2013), Acta Cryst. D69, 1865-1866].

Online 19 November 2013


research papers


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2298-2308  [ doi:10.1107/S0907444913021136 ]

Structure and enzymatic mechanism of a moonlighting dUTPase

I. Leveles, V. Németh, J. E. Szabó, V. Harmat, K. Nyíri, Á. Á. Bendes, V. Papp-Kádár, I. Zagyva, G. Róna, O. Ozohanics, K. Vékey, J. Tóth and B. G. Vértessy

Synopsis: Horizontal gene transfer in some Staphyloccal phages is regulated by phage dUTPases, which are also responsible for maintaining genome integrity. Insights into the molecular mechanism of this regulation as well as into the enzymatic action of [Phi]11 phage dUTPase is provided by three-dimensional structural and enzyme kinetics studies.

PDB reference: 4gv8

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2309-2319  [ doi:10.1107/S0907444913021306 ]

Structural basis for a hand-like site in the calcium sensor CatchER with fast kinetics

Y. Zhang, F. Reddish, S. Tang, Y. Zhuo, Y.-F. Wang, J. J. Yang and I. T. Weber

Synopsis: High-resolution crystal structures of the designed calcium sensor CatchER revealed snapshots of calcium and gadolinium ions binding within the designed site in agreement with its fast kinetics.

PDB references: 4l12, 4l13 and 4l1i

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2320-2329  [ doi:10.1107/S0907444913021550 ]

Staphylococcus aureus thiaminase II: oligomerization warrants proteolytic protection against serine proteases

A. Begum, J. Drebes, A. Kikhney, I. B. Müller, M. Perbandt, D. Svergun, C. Wrenger and C. Betzel

Synopsis: The crystal structure of TenA from methicillin-resistant S. aureus, which is a thiaminase type II in the thiamine metabolism of the pathogen and may act as a transcriptional activator controlling the secretion of extracellular proteases, is reported. Mutagenic studies reveal the stabilizing effect of the tetrameric assembly against proteolytic digestion.

PDB reference: 4fn6

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2330-2339  [ doi:10.1107/S0907444913021665 ]

Structural insight into L-ribulose 3-epimerase from Mesorhizobium loti

K. Uechi, H. Sakuraba, A. Yoshihara, K. Morimoto and G. Takata

Synopsis: The structure of L-ribulose 3-epimerase was determined and the unique structural features of the enzyme were compared with those of other ketose 3-epimerases.

PDB reference: 3vyl

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2340-2352  [ doi:10.1107/S0907444913021859 ]

Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a

K. Moncoq, L. Regad, S. Mann, A. Méjean and O. Ploux

Synopsis: The crystal structure of AnaB, the prolyl-acyl carrier protein oxidase involved in anatoxin-a biosynthesis, is reported. The structural basis for the oxidase activity of this flavoprotein with an acyl-CoA dehydrogenase fold is described.

PDB reference: 4irn

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2353-2364  [ doi:10.1107/S0907444913021823 ]

Crystallographic identification of an unexpected protein complex in silkworm haemolymph

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

Synopsis: The crystal structure of a complex of two mulberry silkworm storage proteins, SP2 and SP3, has been determined. The presence of two different proteins in the native complex was detected crystallographically according to electron-density maps.

PDB reference: 4l37

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2365-2380  [ doi:10.1107/S0907444913021975 ]

The landscape of cytokinin binding by a plant nodulin

M. Ruszkowski, K. Szpotkowski, M. Sikorski and M. Jaskolski

Synopsis: The crystal structures of complexes of M. truncatula nodulin 13 with four cytokinins, trans-zeatin, N6-isopentenyladenine, kinetin and N6-benzyladenine, show an unusual mode of dimerization of this PR-10-fold plant protein. The cytokinin-binding mode in the internal cavity of the protein is the same in each complex and resembles the pattern found in the cytokinin receptor protein.

PDB references: 4jhg, 4gy9, 4jhh and 4jhi

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2381-2394  [ doi:10.1107/S0907444913022117 ]

Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies

K. A. Sutton, P. J. Black, K. R. Mercer, E. F. Garman, R. L. Owen, E. H. Snell and W. A. Bernhard

Synopsis: Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage, to confirm a multi-track radiation-damage process and to develop a model of that process.

PDB references: 4h8x, 4h8y, 4h8z, 4h90, 4h91, 4h92, 4h93, 4h94, 4h9a, 4h9b, 4h9c, 4h9e, 4h9f, 4h9h and 4h9i

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2395-2402  [ doi:10.1107/S0907444913022294 ]

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

T. A. P. de Beer, R. A. Laskowski, M.-E. Duban, A. W. E. Chan, W. F. Anderson and J. M. Thornton

Synopsis: LigSearch is a web server for identifying ligands likely to bind to a given protein. It can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2403-2411  [ doi:10.1107/S0907444913022269 ]

Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer

I. Russo Krauss, A. Pica, A. Merlino, L. Mazzarella and F. Sica

Synopsis: The structure of the thrombin-HD22-27mer complex, solved at 2.4 Å resolution, reveals an intriguing duplex-quadruplex folding of the aptamer, which extensively interacts with the exosite II of the protein.

PDB reference: 4i7y

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2412-2419  [ doi:10.1107/S0907444913022397 ]

Structural insights into the role of the Chl4-Iml3 complex in kinetochore assembly

Q. Guo, Y. Tao, H. Liu, M. Teng and X. Li

Synopsis: The Iml3 protein adopts a novel structure to dimerize with the Chl4 in kinetochore assembly.

PDB reference: 4kr1

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2420-2430  [ doi:10.1107/S0907444913022385 ]

The TLR signalling adaptor TRIF/TICAM-1 has an N-­terminal helical domain with structural similarity to IFIT proteins

M. O. Ullah, T. Ve, M. Mangan, M. Alaidarous, M. J. Sweet, A. Mansell and B. Kobe

Synopsis: The structural and functional characterization of the N-terminal domain of the Toll-like receptor signalling adaptor TRIF/TICAM-1 is presented. The 2.22 Å resolution crystal structure was determined by selenomethionine-based SAD phasing using a protein containing two additional introduced methionines.

PDB references: 4bsx and 4c0m

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2431-2439  [ doi:10.1107/S090744491302252X ]

Structural polymorphism in the L1 loop regions of human H2A.Z.1 and H2A.Z.2

N. Horikoshi, K. Sato, K. Shimada, Y. Arimura, A. Osakabe, H. Tachiwana, Y. Hayashi-Takanaka, W. Iwasaki, W. Kagawa, M. Harata, H. Kimura and H. Kurumizaka

Synopsis: The crystal structures of human nucleosomes containing H2A.Z.1 and H2A.Z.2 have been determined. Structural polymorphisms were found in the L1 loop regions of H2A.Z.1 and H2A.Z.2 in the nucleosomes that are likely to be caused by their flexible nature.

PDB references: 3wa9 and 3waa

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Buy article online]

Acta Cryst. (2013). D69, 2440-2450  [ doi:10.1107/S0907444913022683 ]

Structural characterization of the ribonuclease H-­like type ASKHA superfamily kinase MK0840 from Methanopyrus kandleri

M. Schacherl, S. Waltersperger and U. Baumann

Synopsis: The crystal structure of a putative sugar kinase, MK0840, from M. kandleri has been solved in apo and nucleotide-bound forms at high resolution. Large domain movements are observed depending on the crystal form and the nucleotide state.

PDB references: 4bg8, 4bg9, 4bga and 4bgb

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2451-2460  [ doi:10.1107/S0907444913022701 ]

Protein design by fusion: implications for protein structure prediction and evolution

K. Skorupka, S. K. Han, H.-J. Nam, S. Kim and S. Faham

Synopsis: The design of a new protein fold by fusion of a heterodimer is described.

PDB reference: 4iwb

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2461-2467  [ doi:10.1107/S0907444913022579 ]

Structures of native, substrate-bound and inhibited forms of Mycobacterium tuberculosis imidazoleglycerol-phosphate dehydratase

M. S. Ahangar, R. Vyas, N. Nasir and B. K. Biswal

Synopsis: Crystal structures of M. tuberculosis HisB and its substrate-bound and inhibitor-bound forms were determined.

PDB references: 4gqu, 4lom and 4lpf

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2468-2482  [ doi:10.1107/S0907444913022725 ]

Structural basis for type VI secreted peptidoglycan DL-endopeptidase function, specificity and neutralization in Serratia marcescens

V. Srikannathasan, G. English, N. K. Bui, K. Trunk, P. E. F. O'Rourke, V. A. Rao, W. Vollmer, S. J. Coulthurst and W. N. Hunter

Synopsis: Crystal structures of type VI secretion system-associated immunity proteins, a peptidoglycan endopeptidase and a complex of the endopeptidase and its cognate immunity protein are reported together with assays of endopeptidase activity and functional assessment.

PDB references: 4bi3, 4bi4, 4bi8, 3zfi and 3zib

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2483-2494  [ doi:10.1107/S0907444913023196 ]

High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2

T. Murakawa, H. Hayashi, T. Sunami, K. Kurihara, T. Tamada, R. Kuroki, M. Suzuki, K. Tanizawa and T. Okajima

Synopsis: The crystal structure of a copper amine oxidase from A. globiformis was determined at 1.08 Å resolution. Diatomic molecules, most likely to be molecular oxygen, were detected along a route from the central cavity of the dimer interface to the active site.

PDB references: 3wa2 and 3wa3

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]   [RE]  [Buy article online]

Acta Cryst. (2013). D69, 2495-2505  [ doi:10.1107/S0907444913023354 ]

Phosphorylation adjacent to the nuclear localization signal of human dUTPase abolishes nuclear import: structural and mechanistic insights

G. Róna, M. Marfori, M. Borsos, I. Scheer, E. Takács, J. Tóth, F. Babos, A. Magyar, A. Erdei, Z. Bozóky, L. Buday, B. Kobe and B. G. Vértessy

Synopsis: Nucleocytoplasmic trafficking of dUTPase, an enzyme essential for DNA integrity, is regulated by phosphorylation. The mechanism underlying this control is revealed by three-dimensional structures and cellular investigations.

PDB references: 4mz5 and 4mz6

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2506-2512  [ doi:10.1107/S090744491302444X ]

Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain

D. E. Mortenson, D. F. Kreitler, H. G. Yun, S. H. Gellman and K. T. Forest

Synopsis: Two structures of a small protein with a defined tertiary fold, the isolated Pin1 WW domain, have been determined via racemic crystallization with small-molecule additives. These additives, which are either racemic or achiral, appear to stabilize a dynamic loop region of the structure.

PDB references: 4gwt and 4gwv

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2513-2523  [ doi:10.1107/S0907444913024608 ]

Split green fluorescent protein as a modular binding partner for protein crystallization

H. B. Nguyen, L.-W. Hung, T. O. Yeates, T. C. Terwilliger and G. S. Waldo

Synopsis: A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants.

PDB references: 4kf4 and 4kf5

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2524-2533  [ doi:10.1107/S0907444913025250 ]

Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration

W. Awad, G. Svensson Birkedal, M. M. G. M. Thunnissen, K. Mani and D. T. Logan

Synopsis: The anisotropy of crystals of glypican-1 was significantly reduced by controlled dehydration using the HC1 device, allowing the building of previously disordered parts of the structure.

PDB reference: 4bwe

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2534-2542  [ doi:10.1107/S0907444913025997 ]

Protein energy landscapes determined by five-dimensional crystallography

M. Schmidt, V. Srajer, R. Henning, H. Ihee, N. Purwar, J. Tenboer and S. Tripathi

Synopsis: Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings.

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Open access]

Acta Cryst. (2013). D69, 2543-2554  [ doi:10.1107/S0907444913026371 ]

The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis

A. Kumar, S. Kumar, D. Kumar, A. Mishra, R. P. Dewangan, P. Shrivastava, S. Ramachandran and B. Taneja

Synopsis: The structure of Rv3717 determined to 1.7 Å resolution by Pt-SAD phasing reveals a unique autolysin that lacks a cell-wall-binding domain. Rv3717 utilizes its net positive charge for substrate binding and exhibits activity towards a broad spectrum of substrate cell walls. Structural analysis reveals that Rv3717 utilizes a [beta]-hairpin turn at its N-terminus to autoregulate its enzymatic activity.

PDB reference: 4lq6

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2555-2562  [ doi:10.1107/S0907444913027042 ]

Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg2+ cofactor

B. A. Manvilla, E. Pozharski, E. A. Toth and A. C. Drohat

Synopsis: Human AP endonuclease 1 (APE1) belongs to the DNase I-like superfamily of enzymes that require divalent cation(s) to catalyze phosphoryl-transfer reactions. A new 1.92 Å resolution crystal structure of APE1 reveals ideal octahedral coordination of a single Mg2+ ion and informs on the role of this essential cofactor.

PDB reference: 4lnd

Online 19 November 2013


thumbnail of article figure

[HTML version][PDF version][Supplementary Material][Video data file]  [Open access]

Acta Cryst. (2013). D69, 2563-2579  [ doi:10.1107/S0907444913028473 ]

Structural basis of SUFU-GLI interaction in human Hedgehog signalling regulation

A. L. Cherry, C. Finta, M. Karlström, Q. Jin, T. Schwend, J. Astorga-Wells, R. A. Zubarev, M. Del Campo, A. R. Criswell, D. de Sanctis, L. Jovine and R. Toftgård

Synopsis: Crystal and small-angle X-ray scattering structures of full-length human SUFU alone and in complex with the conserved SYGHL motif from GLI transcription factors show major conformational changes associated with binding and reveal an intrinsically disordered region crucial for pathway activation.

PDB references: 4bl8, 4bl9, 4bla, 4blb and 4bld

Online 19 November 2013


short communications


thumbnail of article figure

[HTML version][PDF version][Supplementary Material]  [Buy article online]

Acta Cryst. (2013). D69, 2580-2582  [ doi:10.1107/S0907444913018751 ]

Improving the soluble expression of recombinant proteins by randomly shuffling 5' and 3' coding-sequence ends

C. Bignon, C. Li, J. Lichière, B. Canard and B. Coutard

Synopsis: Using basic technologies available in any laboratory, a method named `boundary shuffling' has been devised to generate orientated libraries for soluble domain selection.

Online 19 November 2013


addenda and errata


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2583  [ doi:10.1107/S0907444913029259 ]

A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel. Erratum

H.-L. Cao, L.-H. Sun, J. Li, L. Tang, H.-M. Lu, Y.-Z. Guo, J. He, Y.-M. Liu, X.-Z. Xie, H.-F. Shen, C.-Y. Zhang, W.-H. Guo, L.-J. Huang, P. Shang, J.-H. He and D.-C. Yin

Synopsis: A correction is made to the article by Cao et al. [(2013), Acta Cryst. D69, 1901-1910].

Online 19 November 2013


 

[HTML version][PDF version]  [Open access]

Acta Cryst. (2013). D69, 2584  [ doi:10.1107/S0907444913029247 ]

Structure analysis of geranyl pyrophos­phate methyltransferase and the proposed reaction mechanism of SAM-dependent C-methylation. Corrigendum

O. Ariyawutthiphan, T. Ose, A. Minami, S. Shinde, M. Tsuda, Y.-G. Gao, M. Yao, H. Oikawa and I. Tanaka

Synopsis: A correction is made to the article by Ariyawutthiphan et al. [(2012), Acta Cryst. D68, 1558-1569].

Online 19 November 2013


Copyright © International Union of Crystallography
IUCr Webmaster