Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 1 (January 2013)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Cover illustrations from each of the 20 years of Acta Cryst. D.

editorial


 

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Acta Cryst. (2013). D69, 1  [ doi:10.1107/S0907444912051190 ]

Celebrating biological crystallography: Acta D twenty years on

E. N. Baker and Z. Dauter

Synopsis: Editorial.

Online 20 December 2012


scientific comment


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Acta Cryst. (2013). D69, 2-4  [ doi:10.1107/S0907444912044794 ]

Placement of molecules in (not out of) the cell

Z. Dauter

Synopsis: The importance of presenting macromolecular structures in unified, standard ways is discussed.

Online 20 December 2012


research papers


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Acta Cryst. (2013). D69, 5-15  [ doi:10.1107/S0907444912039881 ]

A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site

T. Yanagisawa, T. Sumida, R. Ishii and S. Yokoyama

Synopsis: Structural snapshots of the pre- and post-aminoacyl-tRNA synthesis stages have been captured by X-ray crystallography of a novel crystal form of pyrrolysyl-tRNA synthetase.

PDB references: 3vqw, 3vqx and 3vqy

Online 20 December 2012


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Acta Cryst. (2013). D69, 16-23  [ doi:10.1107/S0907444912041005 ]

Structure and activity of the Streptococcus pyogenes family GH1 6-phospho-[beta]-glucosidase SPy1599

J. Stepper, J. Dabin, J. M. Eklof, P. Thongpoo, P. Kongsaeree, E. J. Taylor, J. P. Turkenburg, H. Brumer and G. J. Davies

Synopsis: The S. pyogenes ORF SPy1599, classified into CAZy family GH1, has been shown to display 6-phospho-[beta]-glucosidase activity through a series of kinetics studies on aryl glycosides. The three-dimensional structure has been solved at 2.5 Å resolution from both twinned and untwinned crystal forms.

PDB references: 4b3k and 4b3l

Online 20 December 2012


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Acta Cryst. (2013). D69, 24-31  [ doi:10.1107/S0907444912041169 ]

Structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa

A. Ruf, M. Stihle, J. Benz, M. Schmidt and H. Sobek

Synopsis: The crystal structure of the metalloprotease Gentlyase is described and compared with the structures of other related thermolysin-like proteases.

PDB references: 4ger and 4b52

Online 20 December 2012


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Acta Cryst. (2013). D69, 32-43  [ doi:10.1107/S0907444912042072 ]

Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor

D.-F. Li, J.-Y. Zhang, Y.-J. Hou, L. Liu, Y. Hu, S.-J. Liu, D.-C. Wang and W. Liu

Synopsis: Crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported.

PDB references: 3vsg, 3vsh, 3vsi and 3vsj

Online 20 December 2012


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Acta Cryst. (2013). D69, 44-51  [ doi:10.1107/S0907444912042059 ]

The structure of the deacetylase domain of Escherichia coli PgaB, an enzyme required for biofilm formation: a circularly permuted member of the carbohydrate esterase 4 family

T. Nishiyama, H. Noguchi, H. Yoshida, S.-Y. Park and J. R. H. Tame

Synopsis: Biofilm is an extracellular matrix created by many microorganisms, and a major problem in clinical and technical settings. The crystal structure reported here helps elucidate the synthesis of the major component of biofilm produced by Y. pestis and E. coli, and may assist in the development of agents to block it.

PDB reference: 3vus

Online 20 December 2012


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Acta Cryst. (2013). D69, 52-62  [ doi:10.1107/S0907444912042175 ]

Structures of an active-site mutant of a plant 1,3-[beta]-glucanase in complex with oligosaccharide products of hydrolysis

A. Wojtkowiak, K. Witek, J. Hennig and M. Jaskolski

Synopsis: Two crystal structures of a plant endo-1,3-[beta]-glucanase representing glycoside hydrolase family GH17 in complexes with products of laminarahexose hydrolysis reveal the protein-saccharide interactions at five key binding subsites for the first time. A trisaccharide is bound at subsites -3, -2 and -1 of the nonreducing end (glycon portion) in both structures, and in one structure an extra tetrasaccharide is bound at subsites +1 to +4 of the reducing end (aglycon portion).

PDB references: 4gzi and 4gzj

Online 20 December 2012


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Acta Cryst. (2013). D69, 63-73  [ doi:10.1107/S0907444912042400 ]

The structure of a novel glucuronoyl esterase from Myceliophthora thermophila gives new insights into its role as a potential biocatalyst

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

Synopsis: The crystal structures of an M. thermophila glucuronoyl esterase (StGE2) and of its S213A mutant in the unliganded form and in complex with methyl 4-O-methyl-[beta]-D-glucopyranuronate determined at 1.55, 1.90 and 2.35 Å resolution, respectively, are presented for the first time, disclosing the role of StGE2 as a potential biocatalyst.

PDB references: 4g4g, 4g4i and 4g4j

Online 20 December 2012


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Acta Cryst. (2013). D69, 74-81  [ doi:10.1107/S0907444912042503 ]

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

E. L. DeWalt, V. J. Begue, J. A. Ronau, S. Z. Sullivan, C. Das and G. J. Simpson

Synopsis: Polarization-resolved second-harmonic generation microscopy is applied to the identification of multiple crystalline domains within protein-crystal samples.

Online 20 December 2012


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Acta Cryst. (2013). D69, 82-91  [ doi:10.1107/S0907444912042369 ]

High-resolution structures of AidH complexes provide insights into a novel catalytic mechanism for N-acyl homoserine lactonase

A. Gao, G. Mei, S. Liu, P. Wang, Q. Tang, Y. Liu, H. Wen, X. An, L. Zhang, X. Yan and D. Liang

Synopsis: Crystal structures of the AHL-lactonase AidH in complex with substrate and product are reported at high resolution and a catalytic mechanism is proposed for the metal-independent AHL-lactonase.

PDB references: 4g5x, 4g9e, 4g8d, 4g8b, 4g9g and 4g8c

Online 20 December 2012


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Acta Cryst. (2013). D69, 92-104  [ doi:10.1107/S0907444912043429 ]

Structure of a C-terminal AHNAK peptide in a 1:2:2 complex with S100A10 and an acetylated N-terminal peptide of annexin A2

G. Ozorowski, S. Milton and H. Luecke

Synopsis: Structure of a 20-amino-acid peptide of AHNAK bound asymmetrically to the AnxA2-S100A10A heterotetramer (1:2:2 symmetry) provides insights into the atomic level interactions that govern this membrane-repair scaffolding complex.

PDB reference: 4ftg

Online 20 December 2012


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Acta Cryst. (2013). D69, 105-113  [ doi:10.1107/S0907444912043326 ]

Structure and ligand-binding properties of the biogenic amine-binding protein from the saliva of a blood-feeding insect vector of Trypanosoma cruzi

X. Xu, B. W. Chang, B. J. Mans, J. M. C. Ribeiro and J. F. Andersen

Synopsis: Biogenic amine-binding proteins mediate the anti-inflammatory and antihemostatic activities of blood-feeding insect saliva. The structure of the amine-binding protein from R. prolixus reveals the interaction of biogenic amine ligands with the protein.

PDB references: 4get, 4ge1 and 4hfo

Online 20 December 2012


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Acta Cryst. (2013). D69, 114-120  [ doi:10.1107/S0907444912043880 ]

Structural characterization of Spinacia oleracea trypsin inhibitor III (SOTI-III)

B. Glotzbach, S. Schmelz, M. Reinwarth, A. Christmann, D. W. Heinz and H. Kolmar

Synopsis: The crystal structure of SOTI-III in complex with bovine pancreatic trypsin has been solved to 1.7 Å resolution.

PDB references: 4aor and 4aoq

Online 20 December 2012


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Acta Cryst. (2013). D69, 121-125  [ doi:10.1107/S090744491204423X ]

The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation

J. R. Helliwell and S. W. M. Tanley

Synopsis: The anticancer agents cisplatin and carboplatin bind to a free histidine in a protein. This crystal structure study at data-collection temperatures of 100 and 300 K examines their relative binding affinities to a histidine side chain and the effect of a high radiation dose on the stability of the subsequent protein-Pt adducts. Cisplatin binding is visible and carboplatin binding is not, indicating stronger binding of cisplatin.

PDB references: 4gcb, 4gcc, 4gcd, 4gce and 4gcf

Online 20 December 2012


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Acta Cryst. (2013). D69, 126-136  [ doi:10.1107/S0907444912044800 ]

Adenosine kinase from Schistosoma mansoni: structural basis for the differential incorporation of nucleoside analogues

L. Romanello, J. F. R. Bachega, A. Cassago, J. Brandão-Neto, R. DeMarco, R. C. Garratt and H. D. Pereira

Synopsis: The structural basis for differential nucleoside-analogue incorporation by S. mansoni and human adenosine kinase is revealed.

PDB references: 3vas, 3vaq, 3uq6, 3uq9 and 4dc3

Online 20 December 2012


short communications


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Acta Cryst. (2013). D69, 137-140  [ doi:10.1107/S0907444912042229 ]

Selective X-ray-induced NO photodissociation in haemoglobin crystals: evidence from a Raman-assisted crystallographic study

A. Merlino, M. R. Fuchs, A. Pica, A. Balsamo, F. S. N. Dworkowski, G. Pompidor, L. Mazzarella and A. Vergara

Synopsis: NO photodissociation in a tetrameric haemoglobin has been detected via Raman microscopy on protein single crystals during X-ray diffraction data collection at different radiation doses.

Online 20 December 2012


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