Faculty Opinions recommendation of Structural basis for inverting the enantioselectivity of arylmalonate decarboxylase revealed by the structural analysis of the Gly74Cys/Cys188Ser mutant in the liganded form.

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

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Structural analysis of the human SYCE2–TEX12 complex provides molecular insights into synaptonemal complex assembly

Open Biology ◽

10.1098/rsob.120099 ◽

2012 ◽

Vol 2 (7) ◽

pp. 120099 ◽

Cited By ~ 33

Author(s):

Owen R. Davies ◽

Joseph D. Maman ◽

Luca Pellegrini

Keyword(s):

Structural Analysis ◽

Synaptonemal Complex ◽

Recurrent Miscarriage ◽

Central Element ◽

Biological Data ◽

Structural Basis ◽

Structural Framework ◽

Chromosome Synapsis ◽

Heterotypic Interactions ◽

Physical Features

The successful completion of meiosis is essential for all sexually reproducing organisms. The synaptonemal complex (SC) is a large proteinaceous structure that holds together homologous chromosomes during meiosis, providing the structural framework for meiotic recombination and crossover formation. Errors in SC formation are associated with infertility, recurrent miscarriage and aneuploidy. The current lack of molecular information about the dynamic process of SC assembly severely restricts our understanding of its function in meiosis. Here, we provide the first biochemical and structural analysis of an SC protein component and propose a structural basis for its function in SC assembly. We show that human SC proteins SYCE2 and TEX12 form a highly stable, constitutive complex, and define the regions responsible for their homotypic and heterotypic interactions. Biophysical analysis reveals that the SYCE2–TEX12 complex is an equimolar hetero-octamer, formed from the association of an SYCE2 tetramer and two TEX12 dimers. Electron microscopy shows that biochemically reconstituted SYCE2–TEX12 complexes assemble spontaneously into filamentous structures that resemble the known physical features of the SC central element (CE). Our findings can be combined with existing biological data in a model of chromosome synapsis driven by growth of SYCE2–TEX12 higher-order structures within the CE of the SC.

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Crystal Structures of Two Coronavirus ADP-Ribose-1″-Monophosphatases and Their Complexes with ADP-Ribose: a Systematic Structural Analysis of the Viral ADRP Domain

Journal of Virology ◽

10.1128/jvi.01862-08 ◽

2008 ◽

Vol 83 (2) ◽

pp. 1083-1092 ◽

Cited By ~ 35

Author(s):

Yuanyuan Xu ◽

Le Cong ◽

Cheng Chen ◽

Lei Wei ◽

Qi Zhao ◽

...

Keyword(s):

Structural Analysis ◽

Crystal Structures ◽

Structural Information ◽

Large Family ◽

Binding Pocket ◽

Structural Basis ◽

Active Site Residues ◽

Replication Process ◽

Functional Studies ◽

Group I

ABSTRACT The coronaviruses are a large family of plus-strand RNA viruses that cause a wide variety of diseases both in humans and in other organisms. The coronaviruses are composed of three main lineages and have a complex organization of nonstructural proteins (nsp's). In the coronavirus, nsp3 resides a domain with the macroH2A-like fold and ADP-ribose-1"-monophosphatase (ADRP) activity, which is proposed to play a regulatory role in the replication process. However, the significance of this domain for the coronaviruses is still poorly understood due to the lack of structural information from different lineages. We have determined the crystal structures of two viral ADRP domains, from the group I human coronavirus 229E and the group III avian infectious bronchitis virus, as well as their respective complexes with ADP-ribose. The structures were individually solved to elucidate the structural similarities and differences of the ADRP domains among various coronavirus species. The active-site residues responsible for mediating ADRP activity were found to be highly conserved in terms of both sequence alignment and structural superposition, whereas the substrate binding pocket exhibited variations in structure but not in sequence. Together with data from a previous analysis of the ADRP domain from the group II severe acute respiratory syndrome coronavirus and from other related functional studies of ADRP domains, a systematic structural analysis of the coronavirus ADRP domains was realized for the first time to provide a structural basis for the function of this domain in the coronavirus replication process.

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The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽

10.3390/molecules26165053 ◽

2021 ◽

Vol 26 (16) ◽

pp. 5053

Author(s):

Alina K. Bakunova ◽

Alena Yu. Nikolaeva ◽

Tatiana V. Rakitina ◽

Tatiana Y. Isaikina ◽

Maria G. Khrenova ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Structural Analysis ◽

Active Site ◽

Active Sites ◽

Structural Basis ◽

Active Site Residues ◽

Type Iv ◽

Fold Type ◽

Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

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Crossing the boundary between face-centred cubic and hexagonal close packed: the structure of nanosized cobalt is unraveled by a model accounting for shape, size distribution and stacking faults, allowing simulation of XRD, XANES and EXAFS

Journal of Applied Crystallography ◽

10.1107/s1600576714015970 ◽

2014 ◽

Vol 47 (5) ◽

pp. 1562-1568 ◽

Cited By ~ 19

Author(s):

Alessandro Longo ◽

Luisa Sciortino ◽

Francesco Giannici ◽

Antonino Martorana

Keyword(s):

Structural Analysis ◽

Size Distribution ◽

Structural Model ◽

Close Packing ◽

Structural Basis ◽

Model Parameters ◽

Edge Structure ◽

X Ray ◽

Two Samples ◽

X Ray Absorption

The properties of nanostructured cobalt in the fields of magnetic, catalytic and biomaterials depend critically on Co close packing. This paper reports a structural analysis of nanosized cobalt based on the whole X-ray diffraction (XRD) pattern simulation allowed by the Debye equation. The underlying structural model involves statistical sequences of cobalt layers and produces simulated XRD powder patterns bearing the concurrent signatures of hexagonal and cubic close packing (h.c.p. and f.c.c.). Shape, size distribution and distance distribution between pairs of atoms are also modelled. The simulation algorithm allows straightforward fitting to experimental data and hence the quantitative assessment of the model parameters. Analysis of two samples having, respectively, h.c.p. and f.c.c. appearance is reported. Extended X-ray absorption fine-structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra are simulated on the basis of the model, giving a tool for the interpretation of structural data complementary to XRD. The outlined structural analysis provides a rigorous structural basis for correlations with magnetic and catalytic properties and an experimental reference forab initiomodelling of these properties.

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Structural basis of ethnic-specific variants of PAX4 associated with type 2 diabetes

10.1101/2020.03.24.006254 ◽

2020 ◽

Author(s):

Jun Hosoe ◽

Ken Suzuki ◽

Takashi Kato ◽

Yukinori Okada ◽

Momoko Horikoshi ◽

...

Keyword(s):

Type 2 Diabetes ◽

Structural Analysis ◽

Japanese Population ◽

Association Studies ◽

Genome Wide Association ◽

Structural Basis ◽

Genome Wide Association Studies ◽

Risk Variants ◽

Genome Wide

AbstractRecently, we conducted genome-wide association studies of type 2 diabetes (T2D) in a Japanese population, which identified 20 novel T2D loci that were not associated with T2D in Europeans. Moreover, nine novel missense risk variants, such as those of PAX4, were not rare in the Japanese population, but rare in Europeans. We report in silico structural analysis of ethnic-specific variants of PAX4, which suggests the pathogenic effect of these variants.

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Structural basis for methyl-donor–dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1422981112 ◽

2015 ◽

Vol 112 (31) ◽

pp. E4197-E4205 ◽

Cited By ~ 39

Author(s):

Takuhiro Ito ◽

Isao Masuda ◽

Ken-ichi Yoshida ◽

Sakurako Goto-Ito ◽

Shun-ichi Sekine ◽

...

Keyword(s):

Crystal Structure ◽

Structural Analysis ◽

Specific Binding ◽

Structural Basis ◽

Dependent Manner ◽

Transfer Rnas ◽

Methyl Donor ◽

Trefoil Knot ◽

Domains Of Life ◽

Trna Methyltransferase

The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in transfer RNAs (tRNAs) with the 36GG37 sequence, using S-adenosyl-l-methionine (AdoMet) as the methyl donor. The m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m1G37-tRNA.

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Structural basis ofDeerpox virus-mediated inhibition of apoptosis

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715009402 ◽

2015 ◽

Vol 71 (8) ◽

pp. 1593-1603 ◽

Cited By ~ 18

Author(s):

Denis R. Burton ◽

Sofia Caria ◽

Bevan Marshall ◽

Michele Barry ◽

Marc Kvansakul

Keyword(s):

Structural Analysis ◽

Ligand Binding ◽

Structural Basis ◽

Inhibitor Of Apoptosis ◽

Defence Mechanism ◽

Partial Obstruction ◽

Host Cell Apoptosis ◽

Infected Cells ◽

Binding Groove ◽

Innate Defence

Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that theDeerpox virusinhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteinsviatwo conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.

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Structural and Mechanistic Insights into the Improvement of the Halotolerance of a Marine Microbial Esterase by Increasing Intra- and Interdomain Hydrophobic Interactions

Applied and Environmental Microbiology ◽

10.1128/aem.01286-17 ◽

2017 ◽

Vol 83 (18) ◽

Cited By ~ 5

Author(s):

Ping-Yi Li ◽

Yi Zhang ◽

Bin-Bin Xie ◽

Yan-Qi Zhang ◽

Jie Hao ◽

...

Keyword(s):

Structural Analysis ◽

Water Activity ◽

Catalytic Domain ◽

Hydrophobic Interactions ◽

Underlying Mechanism ◽

High Salt ◽

Structural Basis ◽

Substrate Affinity ◽

Hydrophobic Residues ◽

High Concentrations

ABSTRACT Halotolerant enzymes are beneficial for industrial processes requiring high salt concentrations and low water activity. Most halophilic proteins are evolved to have reduced hydrophobic interactions on the surface and in the hydrophobic cores for their haloadaptation. However, in this study, we improved the halotolerance of a thermolabile esterase, E40, by increasing intraprotein hydrophobic interactions. E40 was quite unstable in buffers containing more than 0.3 M NaCl, and its k cat and substrate affinity were both significantly reduced in 0.5 M NaCl. By introducing hydrophobic residues in loop 1 of the CAP domain and/or α7 of the catalytic domain in E40, we obtained several mutants with improved halotolerance, and the M3 S202W I203F mutant was the most halotolerant. (“M3” represents a mutation in loop 1 of the CAP domain in which residues R22-K23-T24 of E40 are replaced by residues Y22-K23-H24-L25-S26 of Est2.) Then we solved the crystal structures of the S202W I203F and M3 S202W I203F mutants to reveal the structural basis for their improved halotolerance. Structural analysis revealed that the introduction of hydrophobic residues W202 and F203 in α7 significantly improved E40 halotolerance by strengthening intradomain hydrophobic interactions of F203 with W202 and other residues in the catalytic domain. By further introducing hydrophobic residues in loop 1, the M3 S202W I203F mutant became more rigid and halotolerant due to the formation of additional interdomain hydrophobic interactions between the introduced Y22 in loop 1 and W204 in α7. These results indicate that increasing intraprotein hydrophobic interactions is also a way to improve the halotolerance of enzymes with industrial potential under high-salt conditions. IMPORTANCE Esterases and lipases for industrial application are often subjected to harsh conditions such as high salt concentrations, low water activity, and the presence of organic solvents. However, reports on halotolerant esterases and lipases are limited, and the underlying mechanism for their halotolerance is still unclear due to the lack of structures. In this study, we focused on the improvement of the halotolerance of a salt-sensitive esterase, E40, and the underlying mechanism. The halotolerance of E40 was significantly improved by introducing hydrophobic residues. Comparative structural analysis of E40 and its halotolerant mutants revealed that increased intraprotein hydrophobic interactions make these mutants more rigid and more stable than the wild type against high concentrations of salts. This study shows a new way to improve enzyme halotolerance, which is helpful for protein engineering of salt-sensitive enzymes.

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