[IUCr 2014 Congress]

Acta Crystallographica Section D

Biological Crystallography

Volume 70, Part 7 (July 2014)



[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: The crystal structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer associated protein of Clostridium difficile (p. 1983)

research papers


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Acta Cryst. (2014). D70, 1790-1800  [ doi:10.1107/S1399004714004684 ]

Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution

Z. Luo, M. Dauter and Z. Dauter

Synopsis: An ultrahigh-resolution structure of the Z-DNA dodecamer, solved from the anomalous signal of P atoms, reveals substantial flexibility of the backbone phosphate groups.

PDB reference: 4ocb

Online 24 June 2014


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Acta Cryst. (2014). D70, 1801-1811  [ doi:10.1107/S139900471400830X ]

Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

T. Gangi Setty, C. Cho, S. Govindappa, M. A. Apicella and S. Ramaswamy

Synopsis: Structure-function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding.

PDB references: 4mmp, 4mnp and 4mag

Online 24 June 2014


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Acta Cryst. (2014). D70, 1812-1822  [ doi:10.1107/S1399004714004854 ]

Structure determination of human Fas apoptosis inhibitory molecule and identification of the critical residues linking the interdomain interaction to the anti-apoptotic activity

G. Li, L. Qu, S. Ma, Y. Wu, C. Jin and X. Zheng

Synopsis: The structures of N-terminal and C-terminal domains of the human Fas apoptosis inhibitory molecule were determined. Structural and biochemical analyses of the two domains linked the interdomain interaction to the anti-apoptotic activity.

PDB references: 3mx7 and 2kw1

Online 29 June 2014


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Acta Cryst. (2014). D70, 1823-1831  [ doi:10.1107/S1399004714008475 ]

The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins

N. Numoto, T. Nakagawa, R. Ohara, T. Hasegawa, A. Kita, T. Yoshida, T. Maruyama, K. Imai, Y. Fukumori and K. Miki

Synopsis: The structure of the deoxygenated form of the 400 kDa haemoglobin from the tube worm L. satsuma is reported.

PDB references: 3wct, 3wcu, 3wcv and 3wcw

Online 29 June 2014


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Acta Cryst. (2014). D70, 1832-1843  [ doi:10.1107/S1399004714008463 ]

Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole

P. Asztalos, A. Müller, W. Hölke, H. Sobek and M. G. Rudolph

Synopsis: Crystal structures of wild-type L. enzymogenes LysC and of the K30R variant near the substrate-binding site have been determined in complex with the covalent inhibitor TLCK that mimics a tetrahedral reaction intermediate. H-atom density indicates a hydroxyl group in the oxyanion hole.

PDB references: 4nsy and 4nsv

Online 29 June 2014


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Acta Cryst. (2014). D70, 1844-1853  [ doi:10.1107/S1399004714008578 ]

Automated identification of crystallographic ligands using sparse-density representations

C. G. Carolan and V. S. Lamzin

Synopsis: A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner.

Online 29 June 2014


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Acta Cryst. (2014). D70, 1854-1872  [ doi:10.1107/S1399004714008700 ]

Na+/K+ exchange switches the catalytic apparatus of potassium-dependent plant L-asparaginase

M. Bejger, B. Imiolczyk, D. Clavel, M. Gilski, A. Pajak, F. Marsolais and M. Jaskolski

Synopsis: Three crystal structures of potassium-dependent plant L-asparaginase were solved in complexes with K+, with Na+ and with both cations. A novel alkali metal-binding loop Val111-Ser118 (the activation loop) changes its conformation upon K+/Na+ exchange, leading to a reconfiguration of three key residues, His117, Arg224 and Glu250 (the catalytic switch), to allow or prevent substrate binding in the active site of the enzyme.

PDB references: 4pv2, 4pu6 and 4pv3

Online 29 June 2014


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Acta Cryst. (2014). D70, 1873-1883  [ doi:10.1107/S1399004714008943 ]

Exploiting subtle structural differences in heavy-atom derivatives for experimental phasing

J. Wang, Y. Li and Y. Modis

Synopsis: Small differences between heavy-atom derivatives can be exploited to improve the experimental phasing by treating each derivative as an independent SAD data set and combining these data sets with circular permutable pairs of SIR data sets. The basis for this generally applicable approach is that the effective resolution of isomorphous signals between highly isomorphous derivatives is often much higher than the effective resolution of the anomalous signals of individual derivative data sets.

Online 29 June 2014


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Acta Cryst. (2014). D70, 1884-1897  [ doi:10.1107/S1399004714009018 ]

Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites

R. Chaloupkova, T. Prudnikova, P. Rezacova, Z. Prokop, T. Koudelakova, L. Daniel, J. Brezovsky, W. Ikeda-Ohtsubo, Y. Sato, M. Kuty, Y. Nagata, I. Kuta Smatanova and J. Damborsky

Synopsis: Two halide-binding sites were identified in the crystal structure of the newly isolated haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94. Elimination of the second halide-binding site significantly modified the enzyme substrate specificity, catalytic activity and stability in the presence of chloride salts. A shift in the substrate-specificity class after mutagenesis was demonstrated for the first time for haloalkane dehalogenases.

PDB reference: 4k2a

Online 29 June 2014


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Acta Cryst. (2014). D70, 1898-1906  [ doi:10.1107/S139900471400916X ]

Structure of liganded T-state haemoglobin from cat (Felis silvestris catus), a low oxygen-affinity species, in two different crystal forms

M. Balasubramanian, P. Sathya Moorthy, K. Neelagandan, R. Ramadoss, P. R. Kolatkar and M. N. Ponnuswamy

Synopsis: The structure of liganded cat Hb adopts a T-state-like quaternary structure owing to its ligand binding properties, which includes low cooperativity, ligand affinity and the blunt response to an allosteric effector.

PDB references: 3gqr and 3gqp

Online 29 June 2014


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Acta Cryst. (2014). D70, 1907-1913  [ doi:10.1107/S1399004714009250 ]

Structure of Escherichia coli Grx2 in complex with glutathione: a dual-function hybrid of glutaredoxin and glutathione S-transferase

J. Ye, S. V. Nadar, J. Li and B. P. Rosen

Synopsis: The structure of glutaredoxin 2 (Grx2) from Escherichia coli co-crystallized with glutathione (GSH) at 1.60 Å resolution is reported.

PDB references: 4kx4 and 4ksm

Online 29 June 2014


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Acta Cryst. (2014). D70, 1914-1921  [ doi:10.1107/S1399004714009262 ]

Structural insights into interactions of C/EBP transcriptional activators with the Taz2 domain of p300

P. Bhaumik, J. Davis, J. E. Tropea, S. Cherry, P. F. Johnson and M. Miller

Synopsis: Crystal contacts in the structure of a chimeric protein composed of residues 1723-1818 of p300 Taz2 and residues 37-61 of C/EBP[epsilon] reveal a possible mode of interactions of C/EBP transcriptional activators with p300/CBP.

PDB reference: 3t92

Online 29 June 2014


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Acta Cryst. (2014). D70, 1922-1933  [ doi:10.1107/S1399004714009419 ]

Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630

O. A. Asojo, S. K. Nelson, S. Mootien, Y. Lee, W. C. Rezende, D. A. Hyman, M. M. Matsumoto, S. Reiling, A. Kelleher, M. Ledizet, R. A. Koski and K. G. Anthony

Synopsis: Structures of C. difficile alanine racemase in complex with the PLP cofactor and cycloserine are presented.

PDB references: 4lus, 4lut and 4luy

Online 29 June 2014


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Acta Cryst. (2014). D70, 1934-1943  [ doi:10.1107/S1399004714009468 ]

Crystal structures of an ICAM-5 ectodomain fragment show electrostatic-based homophilic adhesions

R. Recacha, D. Jiménez, L. Tian, R. Barredo, C. G. Gahmberg and J. M. Casasnovas

Synopsis: Crystal structures of Intercellular Cell Adhesion Molecule-5 (ICAM-5) show charge-based homotypic interactions and a potential ICAM-5 cell adhesion complex in neurons.

PDB references: 4oi9, 4oib and 4oia

Online 29 June 2014


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Acta Cryst. (2014). D70, 1944-1953  [ doi:10.1107/S139900471400947X ]

Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling pathway

E. Hwang, H.-K. Cheong, A. U. Mushtaq, H.-Y. Kim, K. J. Yeo, E. Kim, W. C. Lee, K. Y. Hwang, C. Cheong and Y. H. Jeon

Synopsis: The heterodimeric structure of the MST1 and RASSF5 SARAH domains is presented. A comparison of homodimeric and heterodimeric interactions provides a structural basis for the preferential association of the SARAH heterodimer.

PDB references: 4oh8 and 4oh9

Online 29 June 2014


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Acta Cryst. (2014). D70, 1954-1964  [ doi:10.1107/S1399004714009626 ]

Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor (EcR) and ultraspiracle (USP) subunits

B. Ren, T. S. Peat, V. A. Streltsov, M. Pollard, R. Fernley, J. Grusovin, S. Seabrook, P. Pilling, T. Phan, L. Lu, G. O. Lovrecz, L. D. Graham and R. J. Hill

Synopsis: The crystal structure of the heterodimeric ligand-binding domains of the B. ovis ecdysone receptor was solved in the presence of an ecdysteroid and a synthetic methylene lactam insecticide, respectively. Analysis of these structures reveals a new level of conformational flexibility for the ecdysone receptor upon binding of ligands.

PDB references: 4ozr and 4ozt

Online 29 June 2014


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Acta Cryst. (2014). D70, 1965-1976  [ doi:10.1107/S1399004714009638 ]

Structural basis of the transactivation deficiency of the human PPAR[gamma] F360L mutant associated with familial partial lipodystrophy

C. Lori, A. Pasquo, R. Montanari, D. Capelli, V. Consalvi, R. Chiaraluce, L. Cervoni, F. Loiodice, A. Laghezza, M. Aschi, A. Giorgi and G. Pochetti

Synopsis: Elucidation of the crystal structure of the PPAR[gamma] F360L-LT175 complex provides considerable insights into the structural basis of the transactivation deficiency of this mutant, which has been associated with familial partial lipodystrophy.

PDB references: 4l96, 4l98 and 4o8f

Online 29 June 2014


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Acta Cryst. (2014). D70, 1977-1982  [ doi:10.1107/S1399004714009754 ]

Crystallographic phasing with NMR models: an envelope approach

W. Zhang, T. Zhang, H. Zhang and Q. Hao

Synopsis: A new molecular replacement approach is reported utilizing a molecular envelope derived from NMR structures at low resolution.

Online 29 June 2014


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Acta Cryst. (2014). D70, 1983-1993  [ doi:10.1107/S1399004714009997 ]

The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile

W. J. Bradshaw, J. M. Kirby, N. Thiyagarajan, C. J. Chambers, A. H. Davies, A. K. Roberts, C. C. Shone and K. R. Acharya

Synopsis: The crystal structure of Cwp84, an S-layer protein from Clostridium difficile is presented for the first time. The cathepsin L-like fold of cysteine protease domain, a newly observed `lectin-like' domain and several other features are described.

PDB reference: 4ci7

Online 29 June 2014


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Acta Cryst. (2014). D70, 1994-2006  [ doi:10.1107/S139900471401013X ]

Protein phasing at non-atomic resolution by combining Patterson and VLD techniques

R. Caliandro, B. Carrozzini, G. L. Cascarano, G. Comunale, C. Giacovazzo and A. Mazzone

Synopsis: A variety of direct and reciprocal-space techniques have been combined for ab initio phasing of proteins at non-atomic resolution.

Online 29 June 2014


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Acta Cryst. (2014). D70, 2007-2018  [ doi:10.1107/S1399004714010311 ]

Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

C. Eibl, M. Hessenberger, J. Wenger and H. Brandstetter

Synopsis: Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer.

PDB references: 4n1j, 4n1k and 4n1l

Online 29 June 2014


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Acta Cryst. (2014). D70, 2019-2031  [ doi:10.1107/S1399004714010268 ]

Structural elucidation of a dual-activity PAP phosphatase-1 from Entamoeba histolytica capable of hydrolysing both 3'-phosphoadenosine 5'-phosphate and inositol 1,4-bisphosphate

K. Faisal Tarique, S. Arif Abdul Rehman and S. Gourinath

Synopsis: The crystal structures of PAP phosphatase-1 from E. histolytica and its complex with AMP have been determined at 2.1 and 2.6 Å resolution, respectively. This enzyme is a Li+-sensitive Mg2+-dependent inositol polyphosphate 1-phosphatase that catalyses the hydrolysis of both 3'-phosphoadenosine 5'-phosphate and inositol 1,4-bisphosphate.

PDB references: 4o7i and 4hxv

Online 29 June 2014


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Acta Cryst. (2014). D70, 2032-2041  [ doi:10.1107/S1399004714010578 ]

Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold

M. Ruszkowski, J. Sliwiak, A. Ciesielska, J. Barciszewski, M. Sikorski and M. Jaskolski

Synopsis: Two plant cytokinin-specific binding proteins were crystallized in complex with gibberellic acid (GA3), which is an entirely different plant hormone. The crystal structures, determined at high resolution, reveal a highly specific mode of GA3 binding, calling for a revision of the hormone specificity of plant proteins with the PR-10 fold.

PDB references: 4psb and 4q0k

Online 29 June 2014


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Acta Cryst. (2014). D70, 2042-2052  [ doi:10.1107/S1399004714011183 ]

BuD, a helix-loop-helix DNA-binding domain for genome modification

S. Stella, R. Molina, B. López-Méndez, A. Juillerat, C. Bertonati, F. Daboussi, R. Campos-Olivas, P. Duchateau and G. Montoya

Synopsis: Crystal structures of BurrH and the BurrH-DNA complex are reported.

PDB references: 4cj9 and 4cja

Online 29 June 2014


addenda and errata


 

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Acta Cryst. (2014). D70, 2053  [ doi:10.1107/S1399004714013613 ]

Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium. Corrigendum

B.-Y. Yoon, Y.-H. Kim, N. Kim, B.-Y. Yun, J.-S. Kim, J.-H. Lee, H.-S. Cho, K. Lee and N.-C. Ha

Synopsis: A correction is made to the article by Yoon et al. [(2013). D69, 1867-1875].

Online 29 June 2014


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