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Proteins perform functions through interacting with other molecules. However, structural details for most of the protein-ligand interactions are unknown. We present a comparative approach (COFACTOR) to recognize functional sites of protein-ligand interactions using low-resolution protein structural models, based on a global-to-local sequence and structural comparison algorithm. COFACTOR was tested...
The spliceosome is a mega-Dalton ribonucleoprotein (RNP) assembly that processes primary RNA transcripts, producing functional mRNA. The electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes are available; however, the spatial arrangement of the latter within the native spliceosome is not known. We designed a computational procedure to efficiently fit thousands...
Helicases move on DNA via an ATP binding and hydrolysis mechanism coordinated by well-characterized helicase motifs. However, the translocation along single-stranded DNA (ssDNA) and the strand separation of double-stranded (dsDNA) may be loosely or tightly coupled. Dda is a phage T4 SF1B helicase with sequence homology to the Pif1 family of helicases that tightly couples translocation to strand separation...
Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They contain C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal β domains that are embedded in the outer membrane. Here, we identify the domain boundaries of an E. coli intimin β domain and use this information to solve its structure and the β domain structure...
The process of dissimilatory metal reduction shapes our environment on a global scale by using minerals as terminal acceptors in a biological electron transport chain employed by bacteria under anaerobic conditions. In this issue of Structure, Edwards et al. present the structure of an extracellular undecaheme cytochrome involved in the step of electron transfer to metal oxides.
In this issue of Structure, He and colleagues present the crystal structure of the phage T4 Dda helicase bound to DNA, providing new insights into how this protein efficiently couples single-stranded DNA translocation to DNA strand separation.
Escherichia coli export the protein YebF into the extracellular medium by a two-step process. However, as no general outer membrane protein secretion system common to all E. coli strains has been reported, the mechanism of export has remained unclear. Herein, we identify the outer membrane proteins OmpF, OmpC, and OmpX as central to the YebF export mechanism using both genetic and planar lipid bilayer...
pH sensing is crucial for survival of most organisms, yet the molecular basis of such sensing is poorly understood. Here, we present an atomic resolution structure of the periplasmic portion of the acid-sensing chemoreceptor, TlpB, from the gastric pathogen Helicobacter pylori. The structure reveals a universal signaling fold, a PAS domain, with a molecule of urea bound with high affinity. Through...
The Atg12-Atg5 conjugate, which is formed by an ubiquitin-like conjugation system, is essential to autophagosome formation, a central event in autophagy. Despite its importance, the molecular mechanism of the Atg12-Atg5 conjugate formation has not been elucidated. Here, we report the solution and crystal structures of Atg10 and Atg5 homologs from Kluyveromyces marxianus (Km), a thermotolerant yeast...
The E3 ligases recruit substrate proteins for targeted ubiquitylation. Recent insights into the mechanisms of ubiquitylation demonstrate that E3 ligases can possess active regulatory properties beyond those of a simple assembly scaffold. Here, we describe the dimeric structure of the E3 ligase adaptor protein SPOP (speckle-type POZ protein) in complex with the N-terminal domain of Cul3 at 2.4 Å resolution...
Ryanodine Receptors (RyRs) are huge Ca 2+ release channels in the endoplasmic reticulum membrane and form targets for phosphorylation and disease mutations. We present crystal structures of a domain in three RyR isoforms, containing the Ser2843 (RyR1) and Ser2808/Ser2814 (RyR2) phosphorylation sites. The RyR1 domain is the target for 11 disease mutations. Several of these are clustered near...
Voltage-gated Na + (Na V ) channels initiate neuronal action potentials. Na V channels are composed of a transmembrane domain responsible for voltage-dependent Na + conduction and a cytosolic C-terminal domain (CTD) that regulates channel function through interactions with many auxiliary proteins, including fibroblast growth factor homologous factors (FHFs) and calmodulin...
The mismatch repair (MMR) initiation protein MutS forms at least two types of sliding clamps on DNA: a transient mismatch searching clamp (∼1 s) and an unusually stable (∼600 s) ATP-bound clamp that recruits downstream MMR components. Remarkably, direct visualization of single MutS particles on mismatched DNA has not been reported. We have combined real-time particle tracking with fluorescence resonance...
In this issue of Structure, Rood and colleagues report that substrate architecture is a key factor in promoting the complete and processive degradation of the Caulobacter cell cycle regulator PdeA by the protease ClpXP. This investigation highlights the important role that the adaptor protein CpdR serves in regulating presentation of PdeA to ClpXP.
In Caulobacter crescentus, the ClpXP protease degrades several crucial cell-cycle regulators, including the phosphodiesterase PdeA. Degradation of PdeA requires the response regulator CpdR and signals a morphological transition in concert with initiation of DNA replication. Here, we report the structure of a Per-Arnt-Sim (PAS) domain of PdeA and show that it is necessary for CpdR-dependent degradation...
The structure of the complex between the transcription cofactor Vgll1 and the transcription factor TEAD4, the mammalian equivalent of the Drosophila Vestigial and Scalloped, respectively, is determined in this study. Remarkably, Vgll1 interacts with TEAD in a manner similar to the transcription coactivators, as well as oncogenes YAP and TAZ, despite having a varied primary sequence. Vgll1-TEAD complex...
Knowledge of the architecture of DNA ligase IV (LigIV) and interactions with XRCC4 and XLF-Cernunnos is necessary for understanding its role in the ligation of double-strand breaks during nonhomologous end joining. Here we report the structure of a subdomain of the nucleotidyltrasferase domain of human LigIV and provide insights into the residues associated with LIG4 syndrome. We use this structural...
In this issue of Structure, Cho and colleagues provide intriguing insight into the first steps of the DNA mismatch repair process. By using single-molecule techniques, they show that the protein MutS undergoes two different types of diffusion on error-containing DNA in an ATP-dependent way.
Members of the genus Shewanella translocate deca- or undeca-heme cytochromes to the external cell surface thus enabling respiration using extracellular minerals and polynuclear Fe(III) chelates. The high resolution structure of the first undeca-heme outer membrane cytochrome, UndA, reveals a crossed heme chain with four potential electron ingress/egress sites arranged within four domains. Sequence...
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