scholarly journals Structural basis of nucleosomal histone H4 lysine 20 methylation by SET8 methyltransferase

2021 ◽  
Vol 4 (4) ◽  
pp. e202000919
Author(s):  
Cheng-Han Ho ◽  
Yoshimasa Takizawa ◽  
Wataru Kobayashi ◽  
Yasuhiro Arimura ◽  
Hiroshi Kimura ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Essential Role ◽  
Histone H3 ◽  
Underlying Mechanism ◽  
Structural Basis ◽  
Histone H4 ◽  
Nucleosomal Histone

SET8 is solely responsible for histone H4 lysine-20 (H4K20) monomethylation, which preferentially occurs in nucleosomal H4. However, the underlying mechanism by which SET8 specifically promotes the H4K20 monomethylation in the nucleosome has not been elucidated. Here, we report the cryo-EM structures of the human SET8–nucleosome complexes with histone H3 and the centromeric H3 variant, CENP-A. Surprisingly, we found that the overall cryo-EM structures of the SET8–nucleosome complexes are substantially different from the previous crystal structure models. In the complexes with H3 and CENP-A nucleosomes, SET8 specifically binds the nucleosomal acidic patch via an arginine anchor, composed of the Arg188 and Arg192 residues. Mutational analyses revealed that the interaction between the SET8 arginine anchor and the nucleosomal acidic patch plays an essential role in the H4K20 monomethylation activity. These results provide the groundwork for understanding the mechanism by which SET8 specifically accomplishes the H4K20 monomethylation in the nucleosome.

Structural basis for the interaction of BamB with the POTRA3–4 domains of BamA

2016 ◽  
Vol 72 (2) ◽  
pp. 236-244 ◽  
Author(s):  
Zhen Chen ◽  
Li-Hong Zhan ◽  
Hai-Feng Hou ◽  
Zeng-Qiang Gao ◽  
Jian-Hua Xu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Escherichia Coli ◽  
Outer Membrane ◽  
Essential Role ◽  
Biochemical Analysis ◽  
Hydrophobic Interactions ◽  
Outer Membrane Proteins ◽  
Structural Basis ◽  
Conserved Residues ◽  
Bam Complex

InEscherichia coli, the Omp85 protein BamA and four lipoproteins (BamBCDE) constitute the BAM complex, which is essential for the assembly and insertion of outer membrane proteins into the outer membrane. Here, the crystal structure of BamB in complex with the POTRA3–4 domains of BamA is reported at 2.1 Å resolution. Based on this structure, the POTRA3 domain is associated with BamBviahydrogen-bonding and hydrophobic interactions. Structural and biochemical analysis revealed that the conserved residues Arg77, Glu127, Glu150, Ser167, Leu192, Leu194 and Arg195 of BamB play an essential role in interaction with the POTRA3 domain.

scholarly journals Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ko Sato ◽  
Amarjeet Kumar ◽  
Keisuke Hamada ◽  
Chikako Okada ◽  
Asako Oguni ◽  
...  
Keyword(s):  
Histone H3 ◽  
Structural Basis ◽  
Wild Type ◽  
Cryo Electron Microscopy ◽  
Nucleosomal Dna ◽  
Oncogenic Mutations ◽  
Binding Cleft ◽  
Dynamics Simulations ◽  
Nucleosome Binding ◽  
Nucleosomal Histone

AbstractDimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.

scholarly journals Structure study of UHRF1, recoginition of epigenetic marks.

2014 ◽  
Vol 70 (a1) ◽  
pp. C1590-C1590
Author(s):  
Kyohei Arita ◽  
Mariko Ariyoshi ◽  
Kazuya Sugita ◽  
Hidehito Tochio ◽  
Masahiro Shirakawa
Keyword(s):  
Crystal Structure ◽  
Dna Methylation ◽  
Dna Binding ◽  
Histone Modifications ◽  
Dna Methyltransferase ◽  
Histone H3 ◽  
Ring Finger ◽  
Structural Basis ◽  
Epigenetic Marks ◽  
Methylated Dna

Two major epigenetic traits, histone modifications and DNA methylation, regulate various chromatin-template processes in mammals. The pattern of these epigenetic traits is cooperatively established in early embryogenesis and cell development, and inherited during the cell cycle. UHRF1 (also known as Np95 or ICBP90) is believed to play an important role in linking the two major epigenetic traits. UHRF1 has five functional domains, UBL, Tandem Tudor (TTD), pland homeo domain (PHD), SET and RING-associated doain (SRA) and RING finger. To maintain DNA methylation pattern, UHRF1 recognizes hemi-methylated DNA generated during DNA replication through interactions with its SRA domain, and recruit maintenance of DNA methyltransferase Dnmt1 to the site [1], [2]. UHRF1 also recognizes histone H3 containing tri-methylated Lys9 (H3K9me3) via its TTD-PHD moiety. [3]. To obtain the structural basis for recognition of epigenetic marks by UHRF1, we determined the crystal structure of the SRA domain in complex with hemi-methylated DNA. The structure showed that the DNA binding caused a loop and an N-terminal tail of the SRA domain. Interestingly, the methyl-cytosine base at the hemi-methylation site was flipped out from the DNA helix, which has not observed in other DNA binding proteins. These results suggest that the Base flip out mechanism is important event for maintenance of DNA methylation. We also determined the crystal structure of TTD-PHD region of UHRF1 in complex with H3K9me3 peptide. To our surprise, the linker region between the reader modules, which is predicted as an intrinsically disorder, was formed a stable structure with binding to the groove of TTD and plays an essential role in the formation of histone H3 binding hole between the reader modules. The structure revealed how multiple histone modifications were simultaneously decoded by the linked histone reader modules of UHRF1.

scholarly journals Structural basis of dynamic P5CS filaments

2021 ◽  
Author(s):  
Jiale Zhong ◽  
Chen-Jun Guo ◽  
Xian Zhou ◽  
Chia-Chun Chang ◽  
Boqi Yin ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Essential Role ◽  
Point Mutations ◽  
Underlying Mechanism ◽  
Structural Basis ◽  
Multiple Interfaces ◽  
Cryo Electron Microscopy ◽  
Neurocutaneous Syndrome

AbstractThe bifunctional enzyme Δ1-pyrroline-5-carboxylate synthase (P5CS) is central to the synthesis of proline and ornithine. Pathogenic mutations in P5CS gene (ALDH18A1) lead to neurocutaneous syndrome and skin relaxation connective tissue disease in humans, and P5CS deficiency seriously damages the ability to resist adversity in plants, which has an essential role in agriculture and human health. Recently, P5CS has been demonstrated forming the cytoophidium in vivo and filaments in vitro. However, the underlying mechanism for the function of P5CS filamentation and catalyze the synthesis of P5C is hardly accessible without structural basis. Here, we have succeeded in determining the full-length structures of Drosophila P5CS filament in three states at resolution from 3.1 to 4.3 Å under cryo-electron microscopy, we observed the distinct ligand-binding states and conformational changes for GK and GPR domain separately. These structures show the distinctive spiral filament is assembled by P5CS tetramers and stabilized by multiple interfaces. Point mutations that deplete such interactions disturb P5CS filamentation and greatly reduce the activity. Our findings reveal a previously undescribed mechanism that filamentation is crucial for the coordination between GK and GPR domains, and provide insights into structural basis for catalysis function of P5CS filament.

scholarly journals Structural basis for the strict exclusion of proline from the N-glycosylation sequon

2021 ◽  
Author(s):  
Daisuke Kohda ◽  
Yuya Taguchi ◽  
Takahiro Yamasaki ◽  
Marie Ishikawa ◽  
Yuki Kawasaki ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Essential Role ◽  
Ring Structure ◽  
Structural Basis ◽  
Side Chain ◽  
Ramachandran Plot ◽  
Amino Acid Motif ◽  
External Loop ◽  
Backbone Dihedral Angle

Abstract Oligosaccharyltransferase (OST) catalyzes oligosaccharide transfer to the Asn residue in the N-glycosylation sequon, Asn-X-Ser/Thr, where Pro is strictly excluded at position X. Considering the unique structural properties of proline, this exclusion may not be surprising, but the structural basis for the rejection of Pro residues should be explained explicitly. The crystal structure of an archaeal OST in a complex with a sequon-containing peptide and dolichol-phosphate was determined to a 2.7 Å resolution. The sequon part in the peptide forms two inter-chain hydrogen bonds with a conserved amino acid motif, TIXE. We confirmed the essential role of the TIXE motif and the adjacent regions by extensive alanine-scanning of the external loop 5. A Ramachandran plot revealed that the ring structure of the Pro side chain is incompatible with the φ backbone dihedral angle around -150° in the rigid sequon-TIXE structure.

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