July 2014 issue
Acta Cryst. (2014). D70, 1790-1800
Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution
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: d(CGCGCGCGCGCG)2, 4ocb
Acta Cryst. (2014). D70, 1801-1811
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.
Acta Cryst. (2014). D70, 1812-1822
Structure determination of human Fas apoptosis inhibitory molecule and identification of the critical residues linking the interdomain interaction to the anti-apoptotic activity
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: FAIM-S, NTD, 3mx7; CTD, 2kw1
Acta Cryst. (2014). D70, 1823-1831
The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
The structure of the deoxygenated form of the 400 kDa haemoglobin from the tube worm L. satsuma is reported.
Acta Cryst. (2014). D70, 1832-1843
Atomic resolution structure of a lysine-specific endoproteinase from Lysobacter enzymogenes suggests a hydroxyl group bound to the oxyanion hole
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: LysC, wild type, 4nsy; K30R mutant, 4nsv
Acta Cryst. (2014). D70, 1844-1853
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.
Acta Cryst. (2014). D70, 1854-1872
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: PvAspG1–K/Na, 4pv2; PvAspG1–K, 4pu6; PvAspG1–Na, 4pv3
Acta Cryst. (2014). D70, 1873-1883
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.
Acta Cryst. (2014). D70, 1884-1897
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: DbeA, 4k2a
Acta Cryst. (2014). D70, 1898-1906
Structure of liganded T-state haemoglobin from cat (Felis silvestris catus), a low oxygen-affinity species, in two different crystal forms
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: cat haemoglobin at 2.4 Å, 3gqr; cat haemoglobin at 2.0 Å, 3gqp
Acta Cryst. (2014). D70, 1907-1913
Structure of Escherichia coli Grx2 in complex with glutathione: a dual-function hybrid of glutaredoxin and glutathione S-transferase
The structure of glutaredoxin 2 (Grx2) from Escherichia coli co-crystallized with glutathione (GSH) at 1.60 Å resolution is reported.
PDB references: Grx2–GSH complex, 4kx4; Grx2 C9S/C12S mutant, 4ksm
Acta Cryst. (2014). D70, 1914-1921
Structural insights into interactions of C/EBP transcriptional activators with the Taz2 domain of p300
Crystal contacts in the structure of a chimeric protein composed of residues 1723–1818 of p300 Taz2 and residues 37–61 of C/EBP∊ reveal a possible mode of interactions of C/EBP transcriptional activators with p300/CBP.
PDB reference: C/EBP∊-p300 Taz2 chimera, 3t92
Acta Cryst. (2014). D70, 1922-1933
Structural and biochemical analyses of alanine racemase from the multidrug-resistant Clostridium difficile strain 630
Structures of C. difficile alanine racemase in complex with the PLP cofactor and cycloserine are presented.
Acta Cryst. (2014). D70, 1934-1943
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: ICAM-5 D1–D4, 4oi9; 4oib; 4oia
Acta Cryst. (2014). D70, 1944-1953
Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling pathway
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: MST1–RASSF5 SARAH heterodimer, 4oh8; MST2 SARAH homodimer, 4oh9
Acta Cryst. (2014). D70, 1954-1964
Unprecedented conformational flexibility revealed in the ligand-binding domains of the Bovicola ovis ecdysone receptor (EcR) and ultraspiracle (USP) subunits
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.
Acta Cryst. (2014). D70, 1965-1976
Structural basis of the transactivation deficiency of the human PPARγ F360L mutant associated with familial partial lipodystrophy
Elucidation of the crystal structure of the PPARγ 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.
Acta Cryst. (2014). D70, 1977-1982
A new molecular replacement approach is reported utilizing a molecular envelope derived from NMR structures at low resolution.
Acta Cryst. (2014). D70, 1983-1993
The structure of the cysteine protease and lectin-like domains of Cwp84, a surface layer-associated protein from Clostridium difficile
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: Cwp84, 4ci7
Acta Cryst. (2014). D70, 1994-2006
A variety of direct and reciprocal-space techniques have been combined for ab initio phasing of proteins at non-atomic resolution.
Acta Cryst. (2014). D70, 2007-2018
Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions
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: NLRP14 PYD, 4n1j; D86V mutant, 4n1k; L84R mutant, 4n1l
Acta Cryst. (2014). D70, 2019-2031
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
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: PAP phosphatase-1, 4o7i; complex with AMP, 4hxv
Acta Cryst. (2014). D70, 2032-2041
Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with the PR-10 fold
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: VrPhBP–GA3 complex, 4psb; MtPhBP–GA3 complex, 4q0k
Acta Cryst. (2014). D70, 2042-2052
Crystal structures of BurrH and the BurrH–DNA complex are reported.
PDB references: apo BurrH, 4cj9; BurrH–DNA complex, 4cja
addenda and errata
Acta Cryst. (2014). D70, 2053
Structure of the periplasmic copper-binding protein CueP from Salmonella enterica serovar Typhimurium. Corrigendum
A correction is made to the article by Yoon et al. [(2013). D69, 1867–1875].