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binding  cholerae  crystal structure  crystal  dna  domains  magnetite  protein  rubisco  structural  structure  thaliana rubisco  thaliana 
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Preview: Acta Crystallographica Section D

Acta Crystallographica Section D

Acta Crystallographica Section D: Biological Crystallography welcomes the submission of articles covering any aspect of structural biology, with a particular emphasis on the structures of biological macromolecules and the methods used to determine them. R

Published: 2018-01-01


Structure of Rubisco from Arabidopsis thaliana in complex with 2-carboxyarabinitol-1,5-bisphosphate


The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from Arabidopsis thaliana is reported at 1.5 Å resolution. In light of the importance of A. thaliana as a model organism for understanding higher plant biology, and the pivotal role of Rubisco in photosynthetic carbon assimilation, there has been a notable absence of an A. thaliana Rubisco crystal structure. A. thaliana Rubisco is an L8S8 hexadecamer comprising eight plastome-encoded catalytic large (L) subunits and eight nuclear-encoded small (S) subunits. A. thaliana produces four distinct small-subunit isoforms (RbcS1A, RbcS1B, RbcS2B and RbcS3B), and this crystal structure provides a snapshot of A. thaliana Rubisco containing the low-abundance RbcS3B small-subunit isoform. Crystals were obtained in the presence of the transition-state analogue 2-carboxy-d-arabinitol-1,5-bisphosphate. A. thaliana Rubisco shares the overall fold characteristic of higher plant Rubiscos, but exhibits an interesting disparity between sequence and structural relatedness to other Rubisco isoforms. These results provide the structural framework to understand A. thaliana Rubisco and the potential catalytic differences that could be conferred by alternative A. thaliana Rubisco small-subunit isoforms.

The importance of the helical structure of a MamC-derived magnetite-interacting peptide for its function in magnetite formation


Biomineralization is the process of mineral formation by organisms and involves the uptake of ions from the environment in order to produce minerals, with the process generally being mediated by proteins. Most proteins that are involved in mineral interactions are predicted to contain disordered regions containing large numbers of negatively charged amino acids. Magnetotactic bacteria, which are used as a model system for iron biomineralization, are Gram-negative bacteria that can navigate through geomagnetic fields using a specific organelle, the magnetosome. Each organelle comprises a membrane-enveloped magnetic nanoparticle, magnetite, the formation of which is controlled by a specific set of proteins. One of the most abundant of these proteins is MamC, a small magnetosome-associated integral membrane protein that contains two transmembrane α-helices connected by an ∼21-amino-acid peptide. In vitro studies of this MamC peptide showed that it forms a helical structure that can interact with the magnetite surface and affect the size and shape of the growing crystal. Our results show that a disordered structure of the MamC magnetite-interacting component (MamC-MIC) abolishes its interaction with magnetite particles. Moreover, the size and shape of magnetite crystals grown in in vitro magnetite-precipitation experiments in the presence of this disordered peptide were different from the traits of crystals grown in the presence of other peptides or in the presence of the helical MIC. It is suggested that the helical structure of the MamC-MIC is important for its function during magnetite formation.

Crystal structure of the outer membrane protein OmpU from Vibrio cholerae at 2.2 Å resolution


Vibrio cholerae causes a severe disease that kills thousands of people annually. The outer membrane protein OmpU is the most abundant outer membrane protein in V. cholerae, and has been identified as an important virulence factor that is involved in host-cell interaction and recognition, as well as being critical for the survival of the pathogenic V. cholerae in the host body and in harsh environments. The mechanism of these processes is not well understood owing to a lack of the structure of V. cholerae OmpU. Here, the crystal structure of the V. cholerae OmpU trimer is reported to a resolution of 2.2 Å. The protomer forms a 16-β-stranded barrel with a noncanonical N-terminal coil located in the lumen of the barrel that consists of residues Gly32–Ser42 and is observed to participate in forming the second gate in the pore. By mapping the published functional data onto the OmpU structure, the OmpU structure reinforces the notion that the long extracellular loop L4 with a β-hairpin-like motif may be critical for host-cell binding and invasion, while L3, L4 and L8 are crucially implicated in phage recognition by V. cholerae.

The deduced role of a chitinase containing two nonsynergistic catalytic domains


The glycoside hydrolase family 18 chitinases degrade or alter chitin. Multiple catalytic domains in a glycoside hydrolase family 18 chitinase function synergistically during chitin degradation. Here, an insect group III chitinase from the agricultural pest Ostrinia furnacalis (OfChtIII) is revealed to be an arthropod-conserved chitinase that contains two nonsynergistic GH18 domains according to its catalytic properties. Both GH18 domains are active towards single-chained chitin substrates, but are inactive towards insoluble chitin substrates. The crystal structures of each unbound GH18 domain, as well as of GH18 domains complexed with hexa-N-acetyl-chitohexaose or penta-N-acetyl-chitopentaose, suggest that the two GH18 domains possess endo-specific activities. Physiological data indicated that the developmental stage-dependent gene-expression pattern of OfChtIII was the same as that of the chitin synthase OfChsA but significantly different from that of the chitinase OfChtI, which is indispensable for cuticular chitin degradation. Additionally, immunological staining indicated that OfChtIII was co-localized with OfChsA. Thus, OfChtIII is most likely to be involved in the chitin-synthesis pathway.

The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'


Methyl transfer between methyltetrahydrofolate and corrinoid molecules is a key reaction in biology that is catalyzed by a number of enzymes in many prokaryotic and eukaryotic organisms. One classic example of such an enzyme is cobalamin-dependent methionine synthase (MS). MS is a large modular protein that utilizes an SN2-type mechanism to catalyze the chemically challenging methyl transfer from the tertiary amine (N5) of methyltetrahydrofolate to homocysteine in order to form methionine. Despite over half a century of study, many questions remain about how folate-dependent methyltransferases, and MS in particular, function. Here, the structure of the folate-binding (Fol) domain of MS from Thermus thermophilus is reported in the presence and absence of methyltetrahydrofolate. It is found that the methyltetrahydrofolate-binding environment is similar to those of previously described methyltransferases, highlighting the conserved role of this domain in binding, and perhaps activating, the methyltetrahydrofolate substrate. These structural studies further reveal a new distinct and uncharacterized topology in the C-terminal region of MS Fol domains. Furthermore, it is found that in contrast to the canonical TIM-barrel β8α8 fold found in all other folate-binding domains, MS Fol domains exhibit a unique β8α7 fold. It is posited that these structural differences are important for MS function.

A DNA structural alphabet provides new insight into DNA flexibility


DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson–Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum


A revised Table 6 and Supporting Information are provided for the article by Kuzu et al. [(2016), Acta Cryst. D72, 1137–1148].