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Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 9 (September 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Cartoon representation of the TALE AvrBs3-DNA complex structure. The figure shows the protein helical repeats wrapping around the double strand DNA. Each repeat contains the dipeptides responsible of specific DNA recognition (p. 1707). The initial repeats are colored in red, lime, cyan, green and beige to indicate the initial DNA domain building blocks. The specific protein-DNA interactions involve only the coding DNA strand colored in green.

research papers


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Acta Cryst. (2013). D69, 1633-1644  [ doi:10.1107/S0907444913011402 ]

The crystal structure reveals the molecular mechanism of bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (Rv1415) from Mycobacterium tuberculosis

M. Singh, P. Kumar, S. Yadav, R. Gautam, N. Sharma and S. Karthikeyan

Synopsis: This study represents the first crystal structure of bi-functional ribB/ribA enzyme from Mycobacterium tuberculosis.

PDB reference: 4i14

Online 15 August 2013


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Acta Cryst. (2013). D69, 1645-1652  [ doi:10.1107/S0907444913011839 ]

Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain

C. Krintel, K. Harpsøe, L. G. Zachariassen, D. Peters, K. Frydenvang, D. S. Pickering, M. Gajhede and J. S. Kastrup

Synopsis: The crystal structures of the GluA2 ligand-binding domain in complex with the positive allosteric modulator CX516 and its methyl-substituted analogue Me-CX516 show that their binding modes are similar to those of aniracetam and CX614. This supports that CX516 affects receptor deactivation. The structures also show that there is limited space for substitutions at the piperidine ring of CX516.

PDB references: 4iy5 and 4iy6

Online 15 August 2013


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Acta Cryst. (2013). D69, 1653-1664  [ doi:10.1107/S0907444913011712 ]

Structural and functional characterization of the N-terminal domain of the yeast Mg2+ channel Mrs2

M. B. Khan, G. Sponder, B. Sjöblom, S. Svidová, R. J. Schweyen, O. Carugo and K. Djinovic-Carugo

Synopsis: The first structure of the N-terminal domain of the Mg2+ channel Mrs2 in a monomeric form and a pentameric model of Mrs2 generated using the prokaryotic homologue CorA are presented. Gating and metal-sensing residues were proposed based on the model and were validated using mutational and functional studies in vivo.

PDB reference: 3rkg

Online 15 August 2013


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Acta Cryst. (2013). D69, 1665-1676  [ doi:10.1107/S0907444913011773 ]

Fine-tuning of prototype chicken galectins: structure of CG-2 and structure-activity correlations

F. M. Ruiz, I. S. Fernández, L. López-Merino, L. Lagartera, H. Kaltner, M. Menéndez, S. André, D. Solís, H.-J. Gabius and A. Romero

Synopsis: Expression profiling of the three homodimeric (prototype) chicken galectins (CG-1A, CG-1B and CG-2) has raised evidence of distinct functionalities, explaining the interest in a detailed crystallographic analysis of CG-2. Marked differences are found in the ligand-binding site and in the contact pattern within the homodimer interface, underlying a characteristic orientation of the two subunits. Notably, a distinctive trimer of dimers that is unique in all galectin crystal structures reported to date forms the core unit of the crystallographic assembly.

PDB reference: 2ymz

Online 15 August 2013


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Acta Cryst. (2013). D69, 1677-1684  [ doi:10.1107/S0907444913012687 ]

Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP

L. K. van Geersdaele, M. A. Stead, C. M. Harrison, S. B. Carr, H. J. Close, G. O. Rosbrook, S. D. Connell and S. C. Wright

Synopsis: The crystal structure of a novel C-terminal dimerization domain of the cullin-3 adaptor SPOP is reported. The dimerization interfaces of the SPOP BTB and C-terminal domains act in tandem to generate high-order oligomers that enhance the ubiquitination of substrates.

PDB references: 4hs2 and 4j8z

Online 15 August 2013


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Acta Cryst. (2013). D69, 1685-1696  [ doi:10.1107/S090744491301247X ]

Active-site models for complexes of quinolinate synthase with substrates and intermediates

E. V. Soriano, Y. Zhang, K. L. Colabroy, J. M. Sanders, E. C. Settembre, P. C. Dorrestein, T. P. Begley and S. E. Ealick

Synopsis: Structural studies of quinolinate synthase suggest a model for the enzyme-substrate complex and an enzyme-intermediate complex with a [4Fe-4S] cluster.

PDB reference: 4hhe

Online 15 August 2013


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Acta Cryst. (2013). D69, 1697-1706  [ doi:10.1107/S0907444913013085 ]

Structures of free and inhibited forms of the L,D-transpeptidase LdtMt1 from Mycobacterium tuberculosis

S. Correale, A. Ruggiero, R. Capparelli, E. Pedone and R. Berisio

Synopsis: This work reports the crystal structures of the L,D-transpeptidase LdtMt1 from M. tuberculosis in a ligand-free form and in complex with the carbapenem imipenem.

PDB references: 4jmn and 4jmx

Online 15 August 2013


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Acta Cryst. (2013). D69, 1707-1716  [ doi:10.1107/S0907444913016429 ]

Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism

S. Stella, R. Molina, I. Yefimenko, J. Prieto, G. Silva, C. Bertonati, A. Juillerat, P. Duchateau and G. Montoya

Synopsis: The crystal structure of the AvrBs3-DNA complex is reported.

PDB reference: 2ypf

Online 15 August 2013


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Acta Cryst. (2013). D69, 1717-1725  [ doi:10.1107/S0907444913016284 ]

The structure of XIAP BIR2: understanding the selectivity of the BIR domains

C. Lukacs, C. Belunis, R. Crowther, W. Danho, L. Gao, B. Goggin, C. A. Janson, S. Li, S. Remiszewski, A. Schutt, M. K. Thakur, S. K. Singh, S. Swaminathan, R. Pandey, R. Tyagi, R. Gosu, A. V. Kamath and A. Kuglstatter

Synopsis: The high-resolution crystal structures of apo and peptide-bound XIAP BIR2 are presented and compared with BIR3 structures to understand their selectivity. This crystal system can be used to determine the structures of BIR2-inhibitor complexes.

PDB references: 4j3y, 4j45, 4j44, 4j46, 4j47 and 4j48

Online 15 August 2013


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Acta Cryst. (2013). D69, 1726-1737  [ doi:10.1107/S0907444913013425 ]

Structural and functional analyses of a bacterial homologue of hormone-sensitive lipase from a metagenomic library

T. D. Ngo, B. H. Ryu, H. Ju, E. Jang, K. Park, K. K. Kim and T. D. Kim

Synopsis: The crystal structure of Est25, a bacterial homologue of hormone-sensitive lipase (HSL), was determined at 1.49 Å resolution. The biochemical properties of Est25 were investigated to clarify the functional capacities of HSL and the potential applications of Est25 in biotechnology.

PDB reference: 4j7a

Online 15 August 2013


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Acta Cryst. (2013). D69, 1738-1747  [ doi:10.1107/S0907444913012651 ]

Structure-based elucidation of the regulatory mechanism for aminopeptidase activity

H. M. Ta, S. Bae, S. Han, J. Song, T. K. Ahn, S. Hohng, S. Lee and K. K. Kim

Synopsis: Crystallographic, functional and single-molecule studies of aminopeptidase PepS have been presented. Substrate length selectivity imposed by the substrate binding hole is a key in the regulation of the catalytic activity along with residue specificity and active-site repositioning.

PDB references: 4icq, 4icr and 4ics

Online 15 August 2013


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Acta Cryst. (2013). D69, 1748-1757  [ doi:10.1107/S0907444913017162 ]

1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein

I. Kishko, J. Carey, D. Reha, J. Brynda, R. Winkler, B. Harish, R. Guerra, O. Ettrichova, Z. Kukacka, O. Sheryemyetyeva, P. Novak, M. Kuty, I. Kuta Smatanova, R. Ettrich and M. Lapkouski

Synopsis: Diffraction analysis of E. coli WrbA crystallized in the presence of FAD yields the highest resolution structure yet reported, but with FMN bound, Met10 oxidized, and a propeller-twisted isoalloxazine ring.

PDB reference: 3zho

Online 15 August 2013


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Acta Cryst. (2013). D69, 1758-1767  [ doi:10.1107/S0907444913013802 ]

Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX

G. Volkers, J. M. Damas, G. J. Palm, S. Panjikar, C. M. Soares and W. Hinrichs

Synopsis: Crystal structure analyses of the monooxygenase TetX in complex with tigecycline and minocycline support the observation that all clinically available tetracycline antibiotics can be inactivated by enzymatic hydroxylation. Molecular-dynamics simulations of dioxygen diffusion and experimental xenon-binding sites in TetX are compared with respect to putative dioxygen-binding cavities and dioxygen-diffusion pathways.

PDB references: 4a99, 4a6n and 4guv

Online 15 August 2013


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Acta Cryst. (2013). D69, 1768-1779  [ doi:10.1107/S0907444913013875 ]

`In crystallo' substrate binding triggers major domain movements and reveals magnesium as a co-activator of Trypanosoma brucei pyruvate kinase

W. Zhong, H. P. Morgan, I. W. McNae, P. A. M. Michels, L. A. Fothergill-Gilmore and M. D. Walkinshaw

Synopsis: Magnesium bound to T. brucei pyruvate kinase in the presence of the allosteric activator fructose bisphosphate, but in the absence of the substrate phosphoenolpyruvate, is sequestered in a previously undescribed `priming' position adjacent to the active site. In this way, the enzyme is kept in a conformation with a high affinity for the substrate.

PDB references: 4hyw and 4hyv

Online 17 August 2013


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Acta Cryst. (2013). D69, 1780-1788  [ doi:10.1107/S0907444913014418 ]

Analysis of the human cofilin 1 structure reveals conformational changes required for actin binding

M. Klejnot, M. Gabrielsen, J. Cameron, A. Mleczak, S. K. Talapatra, F. Kozielski, A. Pannifer and M. F. Olson

Synopsis: The crystal structure of the human actin-regulating protein cofilin 1, and comparisons with yeast, Chromalveolata and plant homologues that reveal conformational changes required for actin binding, are reported.

PDB reference: 4bex

Online 17 August 2013


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Acta Cryst. (2013). D69, 1789-1797  [ doi:10.1107/S090744491301500X ]

The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones

J.-K. Li, J.-H. Liao, H. Li, C.-I. Kuo, K.-F. Huang, L.-W. Yang, S.-H. Wu and C.-I. Chang

Synopsis: The crystal structure of the intact substrate-recognition domain of a LonC protease shows a large helical hairpin extension (HHE). The HHEs form a basket-like structure on top of the degradation chamber of the LonC protease. The HHE of LonC shares structural and functional similarity to the [alpha]-helical tentacle of the periplasmic chaperone Skp.

PDB reference: 4fwv

Online 17 August 2013


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Acta Cryst. (2013). D69, 1798-1807  [ doi:10.1107/S0907444913014509 ]

High-affinity inhibitors of Zymomonas mobilis tRNA-guanine transglycosylase through convergent optimization

L. J. Barandun, F. Immekus, P. C. Kohler, T. Ritschel, A. Heine, P. Orlando, G. Klebe and F. Diederich

Synopsis: The simultaneous filling of the ribose-33 and ribose-34 pockets at the active site of Z. mobilis tRNA-guanine transglycosylase was investigated using a series of bifunctionalized lin-benzopurine inhibitors. A strong influence of the crystallization protocol on the solvation pattern and the residual mobility of the bound ligands was observed in the cocrystal structures.

PDB references: 4gg9, 4gh1, 4gh3, 4gi4, 4giy and 4gkt

Online 17 August 2013


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Acta Cryst. (2013). D69, 1808-1817  [ doi:10.1107/S0907444913015278 ]

Structure of the inositol-1-phosphate cytidylyltransferase from Thermotoga maritima

O. V. Kurnasov, H.-J.D. Luk, M. F. Roberts and B. Stec

Synopsis: The T. maritima inositol-1-phosphate cytidylyltransferase structure provides insights into its mechanism of forming CDP-inositol and its interaction with the membrane-bound enzyme in the next step of the biosynthesis of the unusual osmolyte di-myo-inositol-1,1'-phosphate in hyperthermophiles.

PDB reference: 4jd0

Online 17 August 2013


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Acta Cryst. (2013). D69, 1818-1825  [ doi:10.1107/S0907444913017812 ]

Peculiarity in crystal packing of anti-HIV lectin actinohivin in complex with [alpha](1-2)mannobiose

K. Suzuki, M. Tsunoda, M. M. Hoque, F. Zhang, J. Jiang, X. Zhang, N. Ohbayashi, H. Tanaka and A. Takénaka

Synopsis: The fully mature anti-HIV lectin actinohivin in complex with the target [alpha](1-2)mannobiose moiety of the high-mannose-type glycans attached to HIV-1 gp120 has been crystallized into two new forms without packing disorder and their X-ray structures reveal the detailed interaction geometry for specific binding to the target HIV-1.

PDB references: 4end and 4g1r

Online 17 August 2013


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Acta Cryst. (2013). D69, 1826-1838  [ doi:10.1107/S0907444913015412 ]

The structure of human [alpha]-2,6-sialyltransferase reveals the binding mode of complex glycans

B. Kuhn, J. Benz, M. Greif, A. M. Engel, H. Sobek and M. G. Rudolph

Synopsis: The first structure of a human [beta]-galactoside [alpha]-2,6-sialyltransferase I was determined by SIRAS phasing using an iodide soak for derivatization. An elongated glycan from a crystallographic neighbour binds to the active site, mimicking a substrate complex. An analysis of the substrate interactions and a comparison with other sialyltransferases allowed the modelling of a Michaelis complex and conclusions on the catalytic mechanism.

PDB references: 4js1 and 4js2

Online 17 August 2013


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Acta Cryst. (2013). D69, 1839-1849  [ doi:10.1107/S0907444913018027 ]

Humidity control and hydrophilic glue coating applied to mounted protein crystals improves X-ray diffraction experiments

S. Baba, T. Hoshino, L. Ito and T. Kumasaka

Synopsis: A new crystal-mounting method has been developed that involves a combination of controlled humid air and polymer glue for crystal coating. This method is particularly useful when applied to fragile protein crystals that are known to be sensitive to subtle changes in their physicochemical environment.

Online 17 August 2013


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Acta Cryst. (2013). D69, 1850-1860  [ doi:10.1107/S0907444913015424 ]

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

V. Z. Pletnev, N. V. Pletneva, K. A. Lukyanov, E. A. Souslova, A. F. Fradkov, D. M. Chudakov, T. Chepurnykh, I. V. Yampolsky, A. Wlodawer, Z. Dauter and S. Pletnev

Synopsis: The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59.

PDB references: 4jf9, 4jge, 4jeo and 4hvf

Online 17 August 2013


short communications


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Acta Cryst. (2013). D69, 1861-1863  [ doi:10.1107/S090744491301648X ]

mrtailor: a tool for PDB-file preparation for the generation of external restraints

T. Gruene

Synopsis: mrtailor is a tool to improve PDB files for the generation of external restraints for refinement.

Online 17 August 2013


addenda and errata


 

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Acta Cryst. (2013). D69, 1864  [ doi:10.1107/S0907444913019859 ]

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium. Corrigendum

M. M. Harding

Synopsis: A correction is made to the article by Harding [(2002) Acta Cryst. D58, 872-874].

Online 15 August 2013


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