Structural Basis for O2Sensing by the Hemerythrin-like Domain of a Bacterial Chemotaxis Protein:  Substrate Tunnel and Fluxional N Terminus†,‡

Biochemistry ◽  
2006 ◽  
Vol 45 (30) ◽  
pp. 9023-9031 ◽  
Author(s):  
Clara E. Isaza ◽  
Radu Silaghi-Dumitrescu ◽  
Ramesh B. Iyer ◽  
Donald M. Kurtz, ◽  
Michael K. Chan
Keyword(s):  
Bacterial Chemotaxis ◽  
Structural Basis ◽  
Protein Substrate ◽  
N Terminus

scholarly journals Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jennifer L Stamos ◽  
Matthew Ling-Hon Chu ◽  
Michael D Enos ◽  
Niket Shah ◽  
William I Weis
Keyword(s):  
Signaling Pathways ◽  
Glycogen Synthase ◽  
Substrate Recognition ◽  
Glycogen Synthase Kinase 3 ◽  
Structural Basis ◽  
Amino Terminus ◽  
Target Sequence ◽  
Inhibitory Peptide ◽  
Conserved Sequence ◽  
N Terminus

Glycogen synthase kinase-3 (GSK-3) is a key regulator of many cellular signaling pathways. Unlike most kinases, GSK-3 is controlled by inhibition rather than by specific activation. In the insulin and several other signaling pathways, phosphorylation of a serine present in a conserved sequence near the amino terminus of GSK-3 generates an auto-inhibitory peptide. In contrast, Wnt/β-catenin signal transduction requires phosphorylation of Ser/Pro rich sequences present in the Wnt co-receptors LRP5/6, and these motifs inhibit GSK-3 activity. We present crystal structures of GSK-3 bound to its phosphorylated N-terminus and to two of the phosphorylated LRP6 motifs. A conserved loop unique to GSK-3 undergoes a dramatic conformational change that clamps the bound pseudo-substrate peptides, and reveals the mechanism of primed substrate recognition. The structures rationalize target sequence preferences and suggest avenues for the design of inhibitors selective for a subset of pathways regulated by GSK-3.

scholarly journals Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase

2021 ◽  
Author(s):  
Mayu Okada ◽  
Yutaka Tateishi ◽  
Eri Nojiri ◽  
Tsutomu Mikawa ◽  
Sundaresan Rajesh ◽  
...  
Keyword(s):  
Structure Determination ◽  
Active Site ◽  
Residual Dipolar Couplings ◽  
Biological Activities ◽  
Protein Structure Determination ◽  
Paramagnetic Nmr ◽  
Structural Basis ◽  
Recognition Mechanism ◽  
N Terminus ◽  
Large Motion

Despite accumulating evidence that protein dynamics is indispensable for understanding the structural basis of biological activities, it remains challenging to visualize the spatial description of the dynamics and to associate transient conformations with their molecular functions. We have developed a new NMR protein structure determination method for the inference of multi-state conformations using multiple types of NMR data, including paramagnetic NMR and residual dipolar couplings, as well as conventional NOEs. Integration of these data in the structure calculation permits delineating accurate ensemble structures of biomacromolecules. Applying the method to the protein yeast ubiquitin hydrolase 1 (YUH1), we find large dynamics of its N-terminus and crossover loop surrounding the active site for ubiquitin-recognition and proteolysis. The N-terminus gets into and out of the crossover loop, suggesting their underlying functional significance. Our results, including those from biochemical analysis, show that large motion surrounding the active site contributes strongly to the efficiency of the enzymatic activity.

scholarly journals Structural Basis of TRPV4 N Terminus Interaction with Syndapin/PACSIN1-3 and PIP2

Structure ◽  
2018 ◽  
Vol 26 (12) ◽  
pp. 1583-1593.e5 ◽  
Author(s):  
Benedikt Goretzki ◽  
Nina A. Glogowski ◽  
Erika Diehl ◽  
Elke Duchardt-Ferner ◽  
Carolin Hacker ◽  
...  
Keyword(s):  
Structural Basis ◽  
N Terminus

scholarly journals Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Ksenia Finogenova ◽  
Jacques Bonnet ◽  
Simon Poepsel ◽  
Ingmar B Schäfer ◽  
Katja Finkl ◽  
...  
Keyword(s):  
Hox Genes ◽  
Structural Basis ◽  
Active Chromatin ◽  
Critical Position ◽  
H3k27 Methylation ◽  
Nucleosomal Dna ◽  
Polycomb Repression ◽  
N Terminus ◽  
Active Genes

Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro. Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.

scholarly journals The Unique N-Terminus of R-Ras Is Required for Rac Activation and Precise Regulation of Cell Migration

2005 ◽  
Vol 16 (5) ◽  
pp. 2458-2469 ◽  
Author(s):  
Stephen P. Holly ◽  
Mark K. Larson ◽  
Leslie V. Parise
Keyword(s):  
Cell Migration ◽  
Cell Movement ◽  
Myeloid Cell ◽  
Cell Spreading ◽  
Full Length ◽  
Structural Basis ◽  
N Terminus ◽  
Cellular Behaviors ◽  
Dependent Cell ◽  
And Migration

The Ras family GTPase, R-Ras, elicits important integrin-dependent cellular behaviors such as adhesion, spreading and migration. While oncogenic Ras GTPases and R-Ras share extensive sequence homology, R-Ras induces a distinct set of cellular behaviors. To explore the structural basis for these differences, we asked whether the unique N-terminal 26 amino acid extension of R-Ras was responsible for R-Ras–specific signaling events. Using a 32D mouse myeloid cell line, we show that full-length R-Ras activates Rac and induces Rac-dependent cell spreading. In contrast, truncated R-Ras lacking its first 26 amino acids fails to activate Rac, resulting in reduced cell spreading. Truncated R-Ras also stimulates more β3 integrin-dependent cell migration than full-length R-Ras, suggesting that the N-terminus may negatively regulate cell movement. However, neither the subcellular localization of R-Ras nor its effects on cell adhesion are affected by the presence or absence of the N-terminus. These results indicate that the N-terminus of R-Ras positively regulates specific R-Ras functions such as Rac activation and cell spreading but negatively regulates R-Ras–mediated cell migration.

scholarly journals Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy

2021 ◽  
Vol 8 ◽  
Author(s):  
Mahmudul Hasan ◽  
Ipsita Banerjee ◽  
Inna Rozman Grinberg ◽  
Britt-Marie Sjöberg ◽  
Derek T. Logan
Keyword(s):  
Ribonucleotide Reductase ◽  
Solution Structure ◽  
Three Dimensional ◽  
Class I ◽  
Structural Basis ◽  
Α Subunit ◽  
Cryo Electron Microscopy ◽  
N Terminus ◽  
Small Domain ◽  
Essential Enzyme

The essential enzyme ribonucleotide reductase (RNR) is highly regulated both at the level of overall activity and substrate specificity. Studies of class I, aerobic RNRs have shown that overall activity is downregulated by the binding of dATP to a small domain known as the ATP-cone often found at the N-terminus of RNR subunits, causing oligomerization that prevents formation of a necessary α2β2 complex between the catalytic (α2) and radical generating (β2) subunits. In some relatively rare organisms with RNRs of the subclass NrdAi, the ATP-cone is found at the N-terminus of the β subunit rather than more commonly the α subunit. Binding of dATP to the ATP-cone in β results in formation of an unusual β4 tetramer. However, the structural basis for how the formation of the active complex is hindered by such oligomerization has not been studied. Here we analyse the low-resolution three-dimensional structures of the separate subunits of an RNR from subclass NrdAi, as well as the α4β4 octamer that forms in the presence of dATP. The results reveal a type of oligomer not previously seen for any class of RNR and suggest a mechanism for how binding of dATP to the ATP-cone switches off catalysis by sterically preventing formation of the asymmetrical α2β2 complex.

scholarly journals Knots can impair protein degradation by ATP-dependent proteases

2017 ◽  
Vol 114 (37) ◽  
pp. 9864-9869 ◽  
Author(s):  
Álvaro San Martín ◽  
Piere Rodriguez-Aliaga ◽  
José Alejandro Molina ◽  
Andreas Martin ◽  
Carlos Bustamante ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Degradation ◽  
Multidomain Proteins ◽  
Methanocaldococcus Jannaschii ◽  
Protein Substrate ◽  
N Terminus ◽  
Extended Length ◽  
Trefoil Knot ◽  
Knotted Protein

ATP-dependent proteases translocate proteins through a narrow pore for their controlled destruction. However, how a protein substrate containing a knotted topology affects this process remains unknown. Here, we characterized the effects of the trefoil-knotted protein MJ0366 from Methanocaldococcus jannaschii on the operation of the ClpXP protease from Escherichia coli. ClpXP completely degrades MJ0366 when pulling from the C-terminal ssrA-tag. However, when a GFP moiety is appended to the N terminus of MJ0366, ClpXP releases intact GFP with a 47-residue tail. The extended length of this tail suggests that ClpXP tightens the trefoil knot against GFP, which prevents GFP unfolding. Interestingly, if the linker between the knot core of MJ0366 and GFP is longer than 36 residues, ClpXP tightens and translocates the knot before it reaches GFP, enabling the complete unfolding and degradation of the substrate. These observations suggest that a knot-induced stall during degradation of multidomain proteins by AAA proteases may constitute a novel mechanism to produce partially degraded products with potentially new functions.

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