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In this issue of Structure, Love et al. report the three-dimensional structures of the RNA-dependent RNA polymerase (RdRp), 3Dpol, from three different human rhinovirus serotypes.
DNA ligase is an enzyme important for DNA repair and replication. Eukaryotic genomes encode ligases requiring ATP as the cofactor; bacterial genomes encode NAD + -dependent ligase. This difference in substrate specificities and the essentiality of NAD + -dependent ligase for bacterial survival make NAD + -dependent ligase a good target for designing highly specific anti-infectives...
Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 Å resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. The structure of apAPH is a symmetric homodimer with each subunit...
Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear metabolism and cell cycle progression in yeast. X-ray structures of the human Senp2 catalytic protease domain and of a covalent thiohemiacetal transition-state complex obtained between the Senp2 catalytic domain and SUMO-1 revealed details of the respective protease and substrate surfaces utilized in interactions...
The chaperonins GroEL and GroES are essential mediators of protein folding. GroEL binds nonnative protein, ATP, and GroES, generating a ternary complex in which protein folding occurs within the cavity capped by GroES (cis-cavity). We determined the crystal structure of the native GroEL-GroES-ADP homolog from Thermus thermophilus, with substrate proteins in the cis-cavity, at 2.8 Å resolution. Twenty-four...
3D domain swapping is increasingly implicated in amyloidosis but also has potential functional advantages in soluble proteins. Indeed, the structure of an NF-κB p50 mutant (Chirgadze et al., 2004) demonstrates that 3D domain swapping can rescue function after a destabilizing mutation. This work has wider implications for the evolution of protein oligomers.
Protein-protein interactions govern a wide range of cellular processes. Molecular recognition responsible for homodimerization and heterodimerization in the rel/NF-κB family of eukaryotic transcription factors relies on a small cluster of hydrophobic residues. We have carried out a structural analysis of six NF-κB p50 dimer interface mutants; one of them revealed a remarkable alteration. One or possibly...
Structure similarity searches using a combinatorial extension appoach revealed that a protein fold structurally related to the sphingolipid binding domain (SBD) of HIV-1 gp120 (V3 loop) is present on pancreatic bile salt-dependent lipase (BSDL). A synthetic peptide derived from the predicted V3-like domain of BSDL interacted with reconstituted monolayers of sphingolipids such as GalCer and GlcCer...
Added-value is the additional information that a model carries with respect to the template structure used for model building. Thousands of single-template models, corresponding to proteins of known structure, were analyzed. The accuracy of structure-derived properties, such as residue accessibility, surface area, electrostatic potential, and others, was determined as a function of template:target...
We present the crystal structure of the catalytic core of human DNA polymerase kappa (hPolκ), the first structure of a human Y-family polymerase. hPolκ is implicated in the proficient extension of mispaired primer termini on undamaged DNAs, and in the extension step of lesion bypass. The structure reveals a stubby “fingers” subdomain, which despite its small size appears to be tightly restrained with...
Assigning function to structures is an important aspect of structural genomics projects, since they frequently provide structures for uncharacterized proteins. Similarities uncovered by structure alignment can suggest a similar function, even in the absence of sequence similarity. For proteins adopting novel folds or those with many functions, this strategy can fail, but functional clues can still...
In this issue of Structure, crystallographic snapshots of a bacterial DNA ligase in complexes with its substrate NAD + and its product NMN are revealed (Gajiwala and Pinko, 2004). The structures illustrate a novel reaction of DNA ligase and highlight the NMN binding site as a target for new antimicrobials.
CTP synthetase (CTPs) catalyzes the last step in CTP biosynthesis, in which ammonia generated at the glutaminase domain reacts with the ATP-phosphorylated UTP at the synthetase domain to give CTP. Glutamine hydrolysis is active in the presence of ATP and UTP and is stimulated by the addition of GTP. We report the crystal structures of Thermus thermophilus HB8 CTPs alone, CTPs with 3SO 42−...
The soil bacterium Pseudomonas putida 86 uses quinoline as a sole source of carbon and energy. Quinoline 2-oxidoreductase (Qor) catalyzes the first metabolic step converting quinoline to 2-oxo-1,2-dihydroquinoline. Qor is a member of the molybdenum hydroxylases. The molybdenum ion is coordinated by two ene-dithiolate sulfur atoms, two oxo-ligands, and a catalytically crucial sulfido-ligand, whose...
AMP nucleosidase (AMN) catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate. The enzyme is found only in prokaryotes, where it plays a role in purine nucleoside salvage and intracellular AMP level regulation. Enzyme activity is stimulated by ATP and suppressed by phosphate. The structure of unliganded AMN was determined at 2.7 Å resolution, and structures of the complexes with either...
UAP56 is an essential eukaryotic pre-mRNA splicing factor and mRNA export factor. The mechanisms of its functions are not well understood. We determined the crystal structures of the N- and C-terminal domains of human UAP56 (comprising 90% of the full-length UAP56) at 1.9 Å resolution. The two domains each have a RecA-like fold and are connected by a flexible linker. The overall fold of each domain...
Subunit B8 from ubiquinone oxidoreductase (complex I) (CI-B8) is one of several nuclear-encoded supernumerary subunits that are not present in bacterial complex I. Its solution structure shows a thioredoxin fold with highest similarities to the human thioredoxin mutant C73S and thioredoxin 2 from Anabeana sp. Interestingly, these proteins contain active sites in the same area, where the disulfide...
The E2 enzymes are key enzymes in the ubiquitin and ubiquitin-like protein ligation pathways. To understand the functionality of the different E2 enzymes, we analyzed 190 protein sequences and 211 structures and electrostatic potentials. Key findings include: The ScUbc1 orthologs are defined by a C-terminal UBA domain. An N-terminal sequence motif that is highly conserved in all E2s except for Cdc34...
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