March 2013 issue
Acta Cryst. (2013). D69, 313-323
Dimeric Sfh3 has structural changes in its binding pocket that are associated with a dimer–monomer state transformation induced by substrate binding
The dimeric structure of Sfh3 (Sec14 family homologue 3 in yeast) is reported for the first time and differs from the Sec14 proteins reported to date, all of which are monomeric.
PDB reference: dimeric Sfh3, 4fmm
Acta Cryst. (2013). D69, 324-332
The structure of B. subtilis YwfH was determined at three conformational steps: the apo form, an apo-like conformation and the NADPH complex. The structures revealed synchronized conformational changes that facilitate cofactor binding and catalytic activity of the enzyme.
PDB references: Bacillus subtilis YwfH, 3u49; 3u4c; 3u4d
Acta Cryst. (2013). D69, 333-344
The crystal structure of the N-terminal domain of human thioredoxin-interacting protein (TXNIP), which belongs to a recently classified α-arrestin protein family, has been determined. This study provides the first structural information on any of the α-arrestins. Although TXNIP adopts a β-arrestin fold as predicted, it is structurally more similar to Vps26 proteins than to β-arrestins, while sharing below 15% pairwise sequence identity with either.
PDB references: N-terminal domain of TXNIP, 4gei; 4gej
Acta Cryst. (2013). D69, 345-351
Direct metal recognition by guanine nucleotide-exchange factor in the initial step of the exchange reaction
The plant Rab5 GTPase homologue ARA7 in complex with its guanine nucleotide-exchange factor VPS9a was crystallized in the presence of GDP and Ca2+, representing an initial intermediate of the exchange reaction.
PDB reference: ARA7-GDP-Ca2+–VPS9a, 4g01
Acta Cryst. (2013). D69, 352-366
The mouse innate immune adaptor protein mSTING adopts a distinct conformation with two novel c-di-GMP binding modes.
PDB references: mSTING-CTD, 4g3l; mSTING-CTD–c-di-GMP complex, 4g4d
Acta Cryst. (2013). D69, 367-372
The structure of virus-like particles of the small RNA phage PRR1 bound to an RNA segment corresponding to a stem-loop that includes the start codon for the replicase gene has been solved and the binding was compared with the related, and better investigated, phage MS2.A.
PDB reference: PRR1, complex with RNA segment, 4ang
Acta Cryst. (2013). D69, 373-380
The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding
The crystal structures of the N-terminal tandem RRM domains of HuR are reported in RNA-free and RNA-bound forms.
PDB references: ARE-binding domains of HuR, 4egl; RNA-bound, 4ed5
Acta Cryst. (2013). D69, 381-387
REACH: Robotic Equipment for Automated Crystal Harvesting using a six-axis robot arm and a micro-gripper
A six-axis robot arm equipped with a micro-gripper is used to harvest protein crystals from their crystallization drops. Once harvested, the sample is inserted into the X-ray beam by the robot for direct data collection.
Acta Cryst. (2013). D69, 388-397
Structure of a human IgA1 Fab fragment at 1.55 Å resolution: potential effect of the constant domains on antigen-affinity modulation
The three-dimensional structure of a human IgA Fab is reported for the first time in three different crystal forms. Compared with a FabG with identical variable domains, the FabA displays a more rigid architecture which can explain the long-distance effects of the constant regions on antigen-binding affinity.
PDB references: FabA, 3m8o; 3qnx; 3qny; FabG, 3qo1; FabG–peptide complex, 3qnz
Acta Cryst. (2013). D69, 398-408
Structure, recombinant expression and mutagenesis studies of the catalase with oxidase activity from Scytalidium thermophilum
The catalytic and oxidative activities of the catalase from Scytalidium thermophilum are likely to be associated with the same haem active centre. The secondary oxidase activity may be a general feature of monofunctional catalases in the absence of hydrogen peroxide. This bifunctionality may provide some advantages for industry if the oxidase activity can be enhanced through engineering or directed evolution.
PDB references: CATPO, native, 4aue; recombinant, 4aum; H82N variant, 4aul; V123F variant, 4aun
Acta Cryst. (2013). D69, 409-419
The binding of Rap1 to DNA induces potassium permanganate hypersensitivity that is driven by a specific Arg residue in Rap1 but is not associated with major DNA distortion.
PDB reference: Rap1–DNA complex, 4gfb
Acta Cryst. (2013). D69, 420-431
Structural basis for the inhibition of Mycobacterium tuberculosis L,D-transpeptidase by meropenem, a drug effective against extensively drug-resistant strains
The crystal structure of M. tuberculosis L,D-transpeptidase (LdtMt2; Rv2518c) has been determined in both ligand-free and meropenem-bound forms. The detailed view of the interactions between meropenem and LdtMt2 will be useful in structure-guided discovery of new antituberculosis drugs.
PDB references: LdtMt2, apo, 4gsq; mercury derivative, 4gsr; meropenem complex, 4gsu
Acta Cryst. (2013). D69, 432-441
The crystal structures of two fragments of the L,D-transpeptidase from M. tuberculosis have been determined at 1.45 and 1.86 Å resolution. The extramembrane part of this enzyme consists of three domains: two domains related to the immunoglobulin fold and a catalytic domain belonging to the ErfK/YbiS/YhnG family at the C-terminus.
PDB references: LtdMt2, AB module, 4hu2; BC module, 4huc
Acta Cryst. (2013). D69, 442-450
Structure of a novel α-amylase AmyB from Thermotoga neapolitana that produces maltose from the nonreducing end of polysaccharides
In this study, the crystal structure of AmyB from T. neapolitana has been determined at 2.4 Å resolution, revealing that the monomeric AmyB comprises domains A, B and C like other α-amylases, but with structural variations.
PDB reference: AmyB, 4gkl
Acta Cryst. (2013). D69, 451-463
The crystal structures of two 6-P-β-glucosidases from the GH1 family were determined in the apo form and in the presence of a 6′-P-salicin substrate, of the reaction product 6-P-β-glucose and of glucose corresponding to the aglycon molecule. The presence of natural ligands enabled the definition of the structural elements responsible for the recognition and hydrolysis of 6′-P-β-glucosides.
PDB references: LpPgb1, 3qom; apo LpPbg1, 4gze; SmBgl, 3pn8; SmBgl–BG6, 4f66; E375Q SmBgl–PSC, 4f79
Acta Cryst. (2013). D69, 464-470
The crystal structure of the C-terminal domain of a putative U32 peptidase from G. thermoleovorans is reported; it is one of the most tightly packed protein structures reported to date.
Acta Cryst. (2013). D69, 471-485
Insights into the mechanism of pyrrole polymerization catalysed by porphobilinogen deaminase: high-resolution X-ray studies of the Arabidopsis thaliana enzyme
The first X-ray analysis of porphobilinogen deaminase from a plant reveals an extensive highly conserved loop region covering the active site that was completely disordered in previous structures. Structural comparisons suggest that the concerted movements of two enzyme domains may be linked to elongation of the substrate and that during the elongation cycle the bound dipyrromethane cofactor or polypyrrole intermediate moves to vacate one of the cofactor subsites such that an incoming pyrrole moiety can bind.
PDB reference: porphobilinogen deaminase, 4htg
Acta Cryst. (2013). D69, 486-489
A rational surface-engineering approach led to the crystal structure determination of ERK2–docking peptide complexes.
PDB references: ERK2_AA–pepRSK1_SQAA, 4h3p; ERK2_AAGS–pepMKK2, 4h3q
Acta Cryst. (2013). D69, 490-492
Obituary for Guy Dodson.