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The ORF YDR533c from Saccharomyces cerevisiae codes for a 25.5 kDa protein of unknown biochemical function. Transcriptome analysis of yeast has shown that this gene is activated in response to various stress conditions together with proteins belonging to the heat shock family. In order to clarify its biochemical function, we determined the crystal structure of YDR533c to 1.85 Å resolution by the single...
In this issue of Structure, researchers reveal new crystal structures of the bacterial reaction center of Rb. sphaeroides R-26.1 containing either no carotenoid or natural or synthetic carotenoid (Roszak et al., 2004). These structures give insight in to the mechanism of carotenoid binding.
Reverse transcriptases (RTs) are multidomain enzymes of variable architecture that couple both RNA- and DNA-directed DNA polymerase activities with an RNase H activity specific for an RNA:DNA hybrid in order to replicate the single-stranded RNA genome of the retrovirus. Previous structural work has been reported for the heterodimeric HIV-1 and HIV-2 RTs. We now report the first crystal structure of...
GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 Å X-ray structure of the GDPMH-Mg 2+ -GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction...
Filamentous actin is organized into bundles and orthogonal networks by the fimbrin/α-actinin superfamily of F-actin crosslinking proteins. The crystal structure of the Arabidopsis thaliana and Schizosaccharomyces pombe fimbrin cores provides the first description of a functional F-actin crosslinking protein and highlights the compact and distinctly asymmetric organization of the fimbrin molecule,...
Cytochrome c peroxidase (CCP) catalyses the reduction of H 2 O 2 to H 2 O, an important step in the cellular detoxification process. The crystal structure of the di-heme CCP from Pseudomonas nautica 617 was obtained in two different conformations in a redox state with the electron transfer heme reduced. Form IN, obtained at pH 4.0, does not contain Ca 2+ and was refined...
A clear wake-up call that we need to improve the crystallographic treatment of partial disorder is provided by DePristo, de Bakker, and Blundell (2004) in the May issue of Structure.
In this issue of Structure, characteristic features that distinguish protein-protein interfaces from noninterface protein surface (Halperin et al., 2004) provide insights into fundamental properties of protein recognition and contribute to improvement of docking methodologies.
In eukaryotes the primary target for cAMP, a ubiquitous second messenger, is cAMP-dependent protein kinase (PKA). Understanding how binding and release of cAMP changes the cAMP binding domains and then triggers long-range allosteric responses is an important challenge. This conformational switching requires structure solutions of cAMP binding domains in cAMP-bound and cAMP-free states. We describe...
We use time-resolved crystallography to observe the structural progression of a bacterial blue light photoreceptor throughout its photocycle. Data were collected from 10 ns to 100 ms after photoactivation of the E46Q mutant of photoactive yellow protein. Refinement of transient chromophore conformations shows that the spectroscopically distinct intermediates are formed via progressive disruption of...
The human L1 endonuclease (L1-EN) is encoded by the non-LTR retrotransposon LINE-1 (L1). L1 is responsible for more than 1.5 million retrotransposition events in the history of the human genome, contributing more than a quarter to human genomic DNA (L1 and Alu elements). L1-EN is related to the well-understood human DNA repair endonuclease APE1, and its nicking specificity is a major determinant for...
Trichomaglin is a protein isolated from root tuber of the plant Maganlin (Trichosanthes Lepiniate, Cucurbitaceae). The crystal structure of trichomaglin has been determined by multiple-isomorphous replacement and refined at 2.2 Å resolution. The X-ray sequence was established, based on electron density combined with the experimentally determined N-terminal sequence, and the sequence information derived...
Dbl proteins are guanine nucleotide exchange factors for Rho GTPases, containing adjacent Dbl homology (DH) and pleckstrin homology (PH) domains. This domain architecture is virtually invariant and typically required for full exchange potential. Several structures of DH/PH fragments bound to GTPases implicate the PH domain in nucleotide exchange. To more fully understand the functional linkage between...
The E. coli trp repressor (trpR) homodimer recognizes its palindromic DNA binding site through a pair of flexible helix-turn-helix (HTH) motifs displayed on an intertwined helical core. Flexible N-terminal arms mediate association between dimers bound to tandem DNA sites. The 2.5 Å X-ray structure of trpR crystallized in 30% (v/v) isopropanol reveals a substantial conformational rearrangement of HTH...
Mitogen and stress-activated kinase-1 (MSK1) is a serine/threonine protein kinase that is activated by either p38 or p42ERK MAPKs in response to stress or mitogenic extracellular stimuli. MSK1 belongs to a family of protein kinases that contain two distinct kinase domains in one polypeptide chain. We report the 1.8 Å crystal structure of the N-terminal kinase domain of MSK1. The crystal structure...
The presented work describes a structural model for integrin homooligomerization, focusing on the transmembrane domains. The two noncovalently linked integrin subunits, α and β, were previously shown to homodimerize or homotrimerize, respectively. Our work is based on published mutational work that induced homotrimerization of β3 integrins. The mutations provided structural restraints for the creation...
In this issue of Structure, polymorphism of an actin binding protein is revealed in the structure of the fimbrin core (Klein et al., 2004), consistent with previous observations suggesting that proteins built from calponin-homology domains have an ability to bind to F-actin in multiple modes.
Mutations in the Lis1 gene result in lissencephaly (smooth brain), a debilitating developmental syndrome caused by the impaired ability of postmitotic neurons to migrate to their correct destination in the cerebral cortex. Sequence similarities suggest that the LIS1 protein contains a C-terminal seven-blade β-propeller domain, while the structure of the N-terminal fragment includes the LisH (Lis-homology)...
The monomeric cupredoxins are a highly divergent family of copper binding electron transport proteins that function in photosynthesis and respiration. To determine how function and structure are conserved in the context of large sequence differences, we have carried out a detailed analysis of the cupredoxins of known structure and their sequence homologs. The common structure of the cupredoxins is...
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