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Bacteriophage PRD1 is unusual, with an internal lipid membrane, but has striking resemblances to adenovirus that include receptor binding spikes. The PRD1 vertex complex contains P2, a 590 residue monomer that binds to receptors on antibiotic-resistant strains of E. coli and so is the functional counterpart to adenovirus fiber. P2 structures from two crystal forms, at 2.2 and 2.4 A resolution, reveal...
E. coli Hsp100 ClpB can disaggregate denatured polypeptides by employing ATP hydrolysis. The ClpB N-terminal domain (ClpBN) has been proposed to play important roles in ClpB molecular chaperone activities. We have determined the crystal structure of ClpBN to 1.95 A resolution by MAD methods. The ClpBN monomer contains two subdomains that have similar folds. The crystal structure revealed a hydrophobic...
Riboflavin kinase (RFK) is an essential enzyme catalyzing the phosphorylation of riboflavin (vitamin B 2 ) to form FMN, an obligatory step in vitamin B 2 utilization and flavin cofactor synthesis. The structure of human RFK revealed a six-stranded antiparallel β barrel core structurally similar to the riboflavin synthase/ferredoxin reductase FAD binding domain fold. The binding site...
Multiple long molecular dynamics simulations are used to probe the oligomerization mechanism of Aβ 16-22 (KLVFFAE) peptides. The peptides, in the monomeric form, adopt either compact random-coil or extended β strand-like structures. The assembly of the low-energy oligomers, in which the peptides form antiparallel β sheets, occurs by multiple pathways with the formation...
Three-dimensional domain swapping is the event by which a monomer exchanges part of its structure with identical monomers to form an oligomer where each subunit has a similar structure to the monomer. The accumulating number of observations of this phenomenon in crystal structures has prompted speculation as to its biological relevance. Domain swapping was originally proposed to be a mechanism for...
In a designed fusion protein the trimeric domain foldon from bacteriophage T4 fibritin was connected to the C terminus of the collagen model peptide (GlyProPro) 10 by a short Gly-Ser linker to facilitate formation of the three-stranded collagen triple helix. Crystal structure analysis at 2.6 A resolution revealed conformational changes within the interface of both domains compared with...
The crystal structure of Rab escort protein (REP) determined in complex with Rab geranylgeranyltransferase (RabGGT), and a new RabGDI-lipid structure shed new light on how these two related proteins recognize different protein components in Rab prenylation and recycling pathways.
In this issue of Structure, Klimov and Thirumalai provide a first glimpse into the forming amyloid nucleus and explain divergent experimental observations of amyloid self-assembly in the initial stages of amyloid formation.
Reef-building corals contain host pigments, termed pocilloporins, that function to regulate the light environment of their resident microalgae by acting as a photoprotectant in excessive sunlight. We have determined the crystal structure of an intensely blue, nonfluorescent pocilloporin to 2.2 A resolution and a genetically engineered fluorescent variant to 2.4 A resolution. The pocilloporin chromophore...
Sliding clamps are loaded onto DNA by ATP-driven clamp loader complexes. The structure of the E. coli clamp loader in a nucleotide-free state has been determined previously. We now report crystal structures of a truncated form of the isolated γ-ATPase subunit, γ 1-243 , of the E. coli clamp loader, in nucleotide-free and bound forms. The γ subunit adopts a defined conformation...
The receptor binding protein P2 of the bacteriophage PRD1 has been shown to consist of a β propeller ''head'' with pseudo-6-fold symmetry and an elongated ''tail'' with a protruding proline-rich ''fin.'' This novel viral receptor binding structure is suggestive of its orientation on the viral capsid and its role in viral entry.
The three-dimensional structure of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii was determined at 1.4 A resolution. The pyruvoyl group of arginine decarboxylase is generated by an autocatalytic internal serinolysis reaction at Ser53 in the proenzyme resulting in two polypeptide chains. The structure of the nonprocessing S53A mutant was also determined. The active site of...
The azalide azithromycin and the ketolide ABT-773, which were derived by chemical modifications of erythromycin, exhibit elevated activity against a number of penicillin- and macrolide-resistant pathogenic bacteria. Analysis of the crystal structures of the large ribosomal subunit from Deinococcus radiodurans complexed with azithromycin or ABT-773 indicates that, despite differences in the number...
In this issue of Structure, a new β barrel kinase fold and a unique structural arrangement for phosphoryl transfer is revealed by Zhang and coworkers through their structure determination of riboflavin kinase.
Rab GTPases, key regulators of membrane targeting and fusion, require the covalent attachment of geranylgeranyl lipids to their C terminus for function. To elucidate the role of lipid in Rab recycling, we have determined the crystal structure of Rab guanine nucleotide dissociation inhibitor (αGDI) in complex with a geranylgeranyl (GG) ligand (H 2 N-Cys-(S-GG)-OMe). The lipid is bound beneath...
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