PDBsum entry 5zmd

Oxidoreductase/DNA

PDB id: 5zmd

Contents

Protein chains

402 a.a.

DNA/RNA

Ligands

OGA ×4

Metals

_MN ×4

Waters ×18

PDB id:

5zmd

Name:

Oxidoreductase/DNA

Title:

Crystal structure of fto in complex with m6da modified ssdna

Structure:

Alpha-ketoglutarate-dependent dioxygenase fto. Chain: a, c, e, g. Synonym: fat mass and obesity-associated protein. Engineered: yes. Mutation: yes. DNA (5'-d(p Tp Cp Tp (6Ma)p Tp Ap Tp Cp G)-3'). Chain: b, d, f, h. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: fto, kiaa1752. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. DNA launch vector pde-gfp2. Organism_taxid: 415098

Resolution:

3.30Å R-factor: 0.272 R-free: 0.292

Authors:

X.Zhang,L.H.Wei,J.Luo,Y.Xiao,J.Liu,W.Zhang,L.Zhang,G.F.Jia

Key ref:

X.Zhang et al. (2019). Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates. Proc Natl Acad Sci U S A, 116, 2919-2924. PubMed id: 30718435 DOI: 10.1073/pnas.1820574116

Date:

02-Apr-18 Release date: 10-Apr-19

Protein chains

Q9C0B1  (FTO_HUMAN) -  Alpha-ketoglutarate-dependent dioxygenase FTO from Homo sapiens

Seq: 505 a.a.

Struc: 402 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chains

T-C-T-6MA-T-A-T-C-G 9 bases

T-C-T-6MA-T-A-T-C-G 9 bases

T-C-T-6MA-T-A-T-C-G 9 bases

T-C-T-6MA-T-A-T-C-G 9 bases

Enzyme reactions

• Enzyme class 1: E.C.1.14.11.- - ?????
• Enzyme class 2: E.C.1.14.11.53 - mRNA N(6)-methyladenine demethylase.
• Reaction: an N₆-methyladenosine in mRNA + 2-oxoglutarate + O2 = an adenosine in mRNA + formaldehyde + succinate + CO2
• Cofactor: Fe(3+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1820574116

Proc Natl Acad Sci U S A 116:2919-2924 (2019)

PubMed id: 30718435

Structural insights into FTO's catalytic mechanism for the demethylation of multiple RNA substrates.

X.Zhang, L.H.Wei, Y.Wang, Y.Xiao, J.Liu, W.Zhang, N.Yan, G.Amu, X.Tang, L.Zhang, G.Jia.

ABSTRACT

FTO demethylates internal N⁶-methyladenosine (m⁶A) and N⁶,2'-O-dimethyladenosine (m⁶A_m; at the cap +1 position) in mRNA, m⁶A and m⁶A_m in snRNA, and N¹-methyladenosine (m¹A) in tRNA in vivo, and in vitro evidence supports that it can also demethylate N⁶-methyldeoxyadenosine (6mA), 3-methylthymine (3mT), and 3-methyluracil (m³U). However, it remains unclear how FTO variously recognizes and catalyzes these diverse substrates. Here we demonstrate-in vitro and in vivo-that FTO has extensive demethylation enzymatic activity on both internal m⁶A and cap m⁶A_m Considering that 6mA, m⁶A, and m⁶A_m all share the same nucleobase, we present a crystal structure of human FTO bound to 6mA-modified ssDNA, revealing the molecular basis of the catalytic demethylation of FTO toward multiple RNA substrates. We discovered that (i) N⁶-methyladenine is the most favorable nucleobase substrate of FTO, (ii) FTO displays the same demethylation activity toward internal m⁶A and m⁶A_m in the same RNA sequence, suggesting that the substrate specificity of FTO primarily results from the interaction of residues in the catalytic pocket with the nucleobase (rather than the ribose ring), and (iii) the sequence and the tertiary structure of RNA can affect the catalytic activity of FTO. Our findings provide a structural basis for understanding the catalytic mechanism through which FTO demethylates its multiple substrates and pave the way forward for the structure-guided design of selective chemicals for functional studies and potential therapeutic applications.