scholarly journals The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

2020 ◽  
Author(s):  
Anna-Lena Steckelberg ◽  
Quentin Vicens ◽  
David A. Costantino ◽  
Jay C. Nix ◽  
Jeffrey S. Kieft
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Rna Structures ◽  
Discrete Elements ◽  
Protein Coding ◽  
Sequence Elements ◽  
Conservation Patterns ◽  
Function Relationship ◽  
Relationship Of ◽  
Folded Rna

ABSTRACTExonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5’ to 3’ exonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

Relationship of the nanocrystal morphology and atomistic structure with respect to the superstructure ordering within PbS- and Gold-Mesocrystals

2014 ◽  
Vol 1705 ◽  
Author(s):  
Lydia Bahrig ◽  
Danny Haubold ◽  
Falk Röder ◽  
Stephen G. Hickey ◽  
Alexander Eychmüller
Keyword(s):  
Crystal Structure ◽  
Structure Formation ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Relationship Of ◽  
The Relationship ◽  
Atomistic Structure

ABSTRACTThe relationship between nanoparticle geometry and their two dimensional assembly is investigated in order to provide insights into the three dimensional arrangement of mesocrystals. The crystal structure of the nanoparticles and their homogeneity are investigated during structure formation on the mesoscale whereby effects such as fibrillation have been observed.

Insights into the relationship between the haem-binding pocket and the redox potential ofc6cytochromes: four atomic resolution structures ofc6andc6-like proteins fromSynechococcussp. PCC 7002

2014 ◽  
Vol 70 (11) ◽  
pp. 2823-2832 ◽  
Author(s):  
Wojciech Bialek ◽  
Szymon Krzywda ◽  
Pawel Zatwarnicki ◽  
Mariusz Jaskolski ◽  
Piotr Kolesinski ◽  
...  
Keyword(s):  
Redox Potential ◽  
Dipole Moments ◽  
Three Dimensional ◽  
Binding Pocket ◽  
High Similarity ◽  
Surface Charge Distribution ◽  
Function Relationship ◽  
Relationship Of ◽  
The Impact ◽  
The Relationship

The structure of cytochromec6Cfrom the mesophilic cyanobacteriumSynechococcussp. PCC 7002 has been determined at 1.03 Å resolution. This is the first structural report on the recently discovered cyanobacterial cytochromec6-like proteins found in marine and nitrogen-fixing cyanobacteria. Despite high similarity in the overall three-dimensional fold between cytochromesc6andc6C, the latter shows saliently different electrostatic properties in terms of surface charge distribution and dipole moments. Its midpoint redox potential is less than half of the value for typicalc6cytochromes and results mainly from the substitution of one residue in the haem pocket. Here, high-resolution crystal structures of mutants of both cytochromesc6andc6Care presented, and the impact of the mutation of specific residues in the haem-binding pocket on the redox potential is discussed. These findings contribute to the elucidation of the structure–function relationship ofc6-like cytochromes.

scholarly journals Structure-function studies of CrmK, an oxidase involved in Caerulomycin A biosynthesis

2014 ◽  
Vol 70 (a1) ◽  
pp. C1669-C1669
Author(s):  
Marie-Ève Picard ◽  
Julie Barma ◽  
Yiguang Zhu ◽  
Xavier Murphy Després ◽  
Jean-Baptiste Duvignaud ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Pocket ◽  
Antimicrobial Activities ◽  
Active Site Residues ◽  
Covalent Bonds ◽  
Protein Residues ◽  
Function Relationship ◽  
Structure And Function Relationship ◽  
And Function ◽  
Relationship Of

Caerulomycin A (CRM A) is an immunosupressive agent that has a unique 2,2'-bipyridine core structure. Isolated from a marine-derived Actinoalloteichus cyanogriseus, this natural product exhibits antifungal, anti-amoebic, antitumor, and antimicrobial activities. Its biosynthetic pathway consists of more than 20 enzymes, at least seven of which are putatively involved in post-PKS/NRPS modifications of the scaffold. Among these, CrmK is a flavin-dependent oxidase. We have determined the crystal structure of CrmK bound to its flavin adenin dinucleotide (FAD) cofactor at 1.9 Å resolution. FAD linkage to CrmK is observed via two covalent bonds with protein residues His64 and Cys124. This crystal structure, combined with the activity analysis of both wild-type CrmK and a series of mutants, has revealed the role of active site residues lining the substrate and FAD binding pocket. Our studies add additional molecular insights into the structure and function relationship of the bicovalently flavinylated oxidases.

scholarly journals X-ray diffraction studies of enkephalins. Crystal structure of [(4′-bromo) Phe4,Leu5]enkephalin

1984 ◽  
Vol 218 (3) ◽  
pp. 677-689 ◽  
Author(s):  
T Ishida ◽  
M Kenmotsu ◽  
Y Mino ◽  
M Inoue ◽  
T Fujiwara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Least Squares Method ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Diffraction Method ◽  
Biologically Active ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Relationship Of

In order to investigate the structure-activity relationship of [Leu5]- and [Met5]enkephalins, [(4′-bromo)Phe4, Leu5]-, [(4′-bromo)Phe4, Met5]- and [Met5] enkephalins were synthesized and crystallized. The crystal structure of [(4′-bromo) Phe4, Leu5]- enkephalin was determined by X-ray diffraction method using the heavy atom method and refined to R = 0.092 by the least-squares method. The molecule in this crystal took essentially the same type I' beta-turn conformation found in [Leu5]enkephalin [Smith & Griffin (1978) Science 199, 1214-1216). On the other hand, the preliminary three-dimensional Patterson analyses showed that the most probable conformations of [(4′-bromo)Phe4,Met5]- and [Met5]enkephalins are both the dimeric extended forms. Based on these insights, the biologically active conformation of enkephalin was discussed in relation to the mu- and delta-receptors.

scholarly journals Pervasiveness of exoribonuclease-resistant RNAs in plant viruses suggests new roles for these conserved RNA structures

2018 ◽  
Author(s):  
Anna-Lena Steckelberg ◽  
Quentin Vicens ◽  
Jeffrey S. Kieft
Keyword(s):  
Plant Viruses ◽  
Untranslated Regions ◽  
Rna Structures ◽  
Protein Coding ◽  
Subgenomic Rnas ◽  
Biochemical Assays ◽  
Intergenic Regions ◽  
Rna Elements ◽  
Folded Rna ◽  
Coding Potential

ABSTRACTExoribonuclease-resistant RNAs (xrRNAs) are discrete folded RNA elements that block the processive degradation of RNA by exoribonucleases. xrRNAs found in the 3′ untranslated regions (UTRs) of animal-infecting flaviviruses and in all three members of the plant-infecting Dianthovirus adopt a complex ring-like fold that blocks the exoribonuclease; this ability gives rise to viral non-coding subgenomic RNAs. The degree to which these folded RNA elements exist in other viruses and in diverse contexts has been unclear. Using computational tools and biochemical assays, we discovered that xrRNA elements are widely found in viruses belonging to the Tombusviridae and Luteoviridae families of plant-infecting RNA viruses, demonstrating their importance and widespread utility. Unexpectedly, many xrRNAs are located in intergenic regions rather than in the 3’UTR and some are associated with the 5′ ends of subgenomic RNAs with protein-coding potential, suggesting that xrRNAs with similar scaffolds are involved in the maturation or maintenance of diverse subgenomic RNAs, not just the ones generated from the 3′UTR.

scholarly journals High-resolution crystal structure of the reduced Grx1 from Saccharomyces cerevisiae

2019 ◽  
Vol 75 (5) ◽  
pp. 392-396 ◽  
Author(s):  
Shadi Maghool ◽  
Sharon La Fontaine ◽  
Megan J. Maher
Keyword(s):  
Crystal Structure ◽  
Saccharomyces Cerevisiae ◽  
Redox Homeostasis ◽  
Redox Status ◽  
Cellular Redox ◽  
Existing Structures ◽  
Structure Solution ◽  
Disulfide Oxidoreductase ◽  
Function Relationship ◽  
Relationship Of

Grx1, a cytosolic thiol–disulfide oxidoreductase, actively maintains cellular redox homeostasis using glutathione substrates (reduced, GSH, and oxidized, GSSG). Here, the crystallization of reduced Grx1 from the yeast Saccharomyces cerevisiae (yGrx1) in space group P212121 and its structure solution and refinement to 1.22 Å resolution are reported. To study the structure–function relationship of yeast Grx1, the crystal structure of reduced yGrx1 was compared with the existing structures of the oxidized and glutathionylated forms. These comparisons revealed structural differences in the conformations of residues neighbouring the Cys27–Cys30 active site which accompany alterations in the redox status of the protein.

scholarly journals Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR

2019 ◽  
Vol 116 (29) ◽  
pp. 14547-14556 ◽  
Author(s):  
Niranjan Varma ◽  
Eshita Mutt ◽  
Jonas Mühle ◽  
Valérie Panneels ◽  
Akihisa Terakita ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Jumping Spider ◽  
Downstream Signaling ◽  
Class A ◽  
Bovine Rhodopsin ◽  
Function Relationship ◽  
Relationship Of ◽  
G Protein Coupled

Light-sensitive G protein-coupled receptors (GPCRs)—rhodopsins—absorb photons to isomerize their covalently bound retinal, triggering conformational changes that result in downstream signaling cascades. Monostable rhodopsins release retinal upon isomerization as opposed to the retinal in bistable rhodopsins that “reisomerize” upon absorption of a second photon. Understanding the mechanistic differences between these light-sensitive GPCRs has been hindered by the scarcity of recombinant models of the latter. Here, we reveal the high-resolution crystal structure of a recombinant bistable rhodopsin, jumping spider rhodopsin-1, bound to the inverse agonist 9-cis retinal. We observe a water-mediated network around the ligand hinting toward the basis of their bistable nature. In contrast to bovine rhodopsin (monostable), the transmembrane bundle of jumping spider rhodopsin-1 as well that of the bistable squid rhodopsin adopts a more “activation-ready” conformation often observed in other nonphotosensitive class A GPCRs. These similarities suggest the role of jumping spider rhodopsin-1 as a potential model system in the study of the structure–function relationship of both photosensitive and nonphotosensitive class A GPCRs.

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