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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Biochemical and structural basis for YTH domain of human YTHDC1 binding to methylated adenine in DNA

The recently characterized mammalian writer (methyltransferase) and eraser (demethylase) of the DNA N6-methyladenine (N6mA) methyl mark act on single-stranded (ss) and transiently-unpaired DNA. As YTH domain-containing proteins bind N6mA-containing RNA in mammalian cells, we investigated whether mammalian YTH domains are also methyl mark readers of N6mA DNA. Here, we show that the YTH domain of YTHDC1 (known to localize in the nucleus) binds ssDNA containing N6mA, with a 10 nM dissociation constant. This binding is stronger by a factor of 5 than in an RNA context, tested under the same conditions. However, the YTH domains of YTHDF2 and YTHDF1 (predominantly cytoplasmic) exhibited the opposite effect with ~1.5–2× stronger binding to ssRNA containing N6mA than to the corresponding DNA. We determined two structures of the YTH domain of YTHDC1 in complex with N6mA-containing ssDNA, which illustrated that YTHDC1 binds the methylated adenine in a single-stranded region flanked by duplexed DNA. We discuss the hypothesis that the writer-reader-eraser of N6mA-containining ssDNA is associated with maintaining genome stability. Structural comparison of YTH and SRA domains (the latter a DNA 5-methylcytosine reader) revealed them to be diverse members of a larger family of DNA/RNA modification readers, apparently having originated from bacterial modification-dependent restriction enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Materials Data on YTh(BRh)8 by Materials Project

ThY(RhB)8 crystallizes in the tetragonal P-4m2 space group. The structure is three-dimensional. Th is bonded in a 12-coordinate geometry to twelve Rh and twelve B atoms. There are four shorter (3.02 Å) and eight longer (3.20 Å) Th–Rh bond lengths. There are eight shorter (3.05 Å) and four longer (3.19 Å) Th–B bond lengths. Y is bonded in a 12-coordinate geometry to twelve Rh and twelve B atoms. There are four shorter (2.99 Å) and eight longer (3.19 Å) Y–Rh bond lengths. There are eight shorter (3.05 Å) and four longer (3.18 Å) Y–B bond lengths. There are two inequivalent Rh sites. In the first Rh site, Rh is bonded in a 5-coordinate geometry to two equivalent Th, one Y, and five B atoms. There are four shorter (2.23 Å) and one longer (2.30 Å) Rh–B bond lengths. In the second Rh site, Rh is bonded in a 5-coordinate geometry to one Th, two equivalent Y, and five B atoms. There are a spread of Rh–B bond distances ranging from 2.23–2.26 Å. There are two inequivalent B sites. In the first B site, B is bonded in a 6-coordinate geometry to two equivalent Th, one Y, five Rh, and one B atom. The B–B bond length is 1.78 Å. In the second B site, B is bonded in a 6-coordinate geometry to one Th, two equivalent Y, five Rh, and one B atom. The B–B bond length is 1.80 Å.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on YTh by Materials Project

ThY crystallizes in the orthorhombic Cmmm space group. The structure is three-dimensional. Th is bonded in a 8-coordinate geometry to four equivalent Th and four equivalent Y atoms. All Th–Th bond lengths are 3.46 Å. All Th–Y bond lengths are 3.49 Å. Y is bonded in a 8-coordinate geometry to four equivalent Th and four equivalent Y atoms. All Y–Y bond lengths are 3.46 Å.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on YTh by Materials Project

ThY is Magnesium-derived structured and crystallizes in the hexagonal P-6m2 space group. The structure is three-dimensional. Th is bonded to six equivalent Th and six equivalent Y atoms to form ThY6Th6 cuboctahedra that share corners with eighteen equivalent ThY6Th6 cuboctahedra, edges with six equivalent ThY6Th6 cuboctahedra, edges with twelve equivalent YY6Th6 cuboctahedra, faces with eight equivalent ThY6Th6 cuboctahedra, and faces with twelve equivalent YY6Th6 cuboctahedra. All Th–Th bond lengths are 3.53 Å. All Th–Y bond lengths are 3.61 Å. Y is bonded to six equivalent Th and six equivalent Y atoms to form YY6Th6 cuboctahedra that share corners with eighteen equivalent YY6Th6 cuboctahedra, edges with six equivalent YY6Th6 cuboctahedra, edges with twelve equivalent ThY6Th6 cuboctahedra, faces with eight equivalent YY6Th6 cuboctahedra, and faces with twelve equivalent ThY6Th6 cuboctahedra. All Y–Y bond lengths are 3.53 Å.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on YTh by Materials Project

ThY is alpha La-derived structured and crystallizes in the trigonal R-3m space group. The structure is three-dimensional. there are three inequivalent Th sites. In the first Th site, Th is bonded to six equivalent Th and six equivalent Y atoms to form ThY6Th6 cuboctahedra that share corners with twelve ThY6Th6 cuboctahedra, edges with twelve ThY6Th6 cuboctahedra, edges with twelve equivalent YY6Th6 cuboctahedra, faces with six equivalent ThY6Th6 cuboctahedra, and faces with twelve equivalent YY6Th6 cuboctahedra. All Th–Th bond lengths are 3.56 Å. All Th–Y bond lengths are 3.57 Å. In the second Th site, Th is bonded to six equivalent Th and six Y atoms to form ThY6Th6 cuboctahedra that share corners with five equivalent YY10Th6 cuboctahedra, corners with twelve ThY6Th6 cuboctahedra, edges with ten YY6Th6 cuboctahedra, edges with twelve ThY6Th6 cuboctahedra, faces with six equivalent ThY6Th6 cuboctahedra, and faces with fifteen YY6Th6 cuboctahedra. All Th–Th bond lengths are 3.56 Å. All Th–Y bond lengths are 3.57 Å. In the third Th site, Th is bonded to six equivalent Th and six Y atoms to form ThY6Th6 cuboctahedra that share corners with five equivalent YY10Th6 cuboctahedra, corners with twelve ThY6Th6 cuboctahedra, edges with ten YY6Th6 cuboctahedra, edges with twelve ThY6Th6 cuboctahedra, faces with six equivalent ThY6Th6 cuboctahedra, and faces with fifteen YY6Th6 cuboctahedra. All Th–Th bond lengths are 3.56 Å. All Th–Y bond lengths are 3.57 Å. There are two inequivalent Y sites. In the first Y site, Y is bonded to six Th and six equivalent Y atoms to form YY6Th6 cuboctahedra that share corners with twelve YY6Th6 cuboctahedra, edges with twelve ThY6Th6 cuboctahedra, edges with twelve YY6Th6 cuboctahedra, faces with six equivalent YY6Th6 cuboctahedra, and faces with twelve ThY6Th6 cuboctahedra. All Y–Y bond lengths are 3.56 Å. In the second Y site, Y is bonded to six Th and ten equivalent Y atoms to form YY10Th6 cuboctahedra that share corners with ten ThY6Th6 cuboctahedra, corners with twelve YY6Th6 cuboctahedra, edges with eight ThY6Th6 cuboctahedra, edges with sixteen YY6Th6 cuboctahedra, faces with sixteen equivalent YY10Th6 cuboctahedra, and faces with eighteen ThY6Th6 cuboctahedra. There are a spread of Y–Y bond distances ranging from 3.56–7.12 Å.

36 MATERIALS SCIENCE↗