PDBsum entry 4y00

DNA binding protein/DNA

PDB id: 4y00

Contents

Protein chains

78 a.a.

DNA/RNA

Waters ×24

PDB id:

4y00

Name:

DNA binding protein/DNA

Title:

Crystal structure of human tdp-43 rrm1 domain with d169g mutation in complex with an unmodified single-stranded DNA

Structure:

Tar DNA-binding protein 43. Chain: a, b, c, d. Fragment: unp residues 101-191. Synonym: tdp-43. Engineered: yes. Mutation: yes. DNA (5'-d(p Tp Tp Gp Ap Gp Cp Gp T)-3'). Chain: e, f, g, h. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tardbp, tdp43. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606

Resolution:

3.00Å R-factor: 0.275 R-free: 0.295

Authors:

C.H.Chiang,P.H.Kuo,W.Z.Yang,H.S.Yuan

Key ref:

C.H.Chiang et al. (2016). Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation. Sci Rep, 6, 21581. PubMed id: 26883171 DOI: 10.1038/srep21581

Date:

05-Feb-15 Release date: 10-Feb-16

Protein chains

Q13148  (TADBP_HUMAN) -  TAR DNA-binding protein 43 from Homo sapiens

Seq: 414 a.a.

Struc: 78 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

T-T-G-A-G-C-G-T 8 bases

G-T-T-G-A-G-C-G-T 9 bases

G-A-G-C 4 bases

C-G-T 3 bases

DOI no: 10.1038/srep21581

Sci Rep 6:21581 (2016)

PubMed id: 26883171

Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation.

C.H.Chiang, C.Grauffel, L.S.Wu, P.H.Kuo, L.G.Doudeva, C.Lim, C.K.Shen, H.S.Yuan.

ABSTRACT

The RNA-binding protein TDP-43 forms intracellular inclusions in amyotrophic lateral sclerosis (ALS). While TDP-43 mutations have been identified in ALS patients, how these mutations are linked to ALS remains unclear. Here we examined the biophysical properties of six ALS-linked TDP-43 mutants and found that one of the mutants, D169G, had higher thermal stability than wild-type TDP-43 and that it was cleaved by caspase 3 more efficiently, producing increased levels of the C-terminal 35 kD fragments (TDP-35) in vitro and in neuroblastoma cells. The crystal structure of the TDP-43 RRM1 domain containing the D169G mutation in complex with DNA along with molecular dynamics simulations reveal that the D169G mutation induces a local conformational change in a β turn and increases the hydrophobic interactions in the RRM1 core, thus enhancing the thermal stability of the RRM1 domain. Our results provide the first crystal structure of TDP-43 containing a disease-linked D169G mutation and a disease-related mechanism showing that D169G mutant is more susceptible to proteolytic cleavage by caspase 3 into the pathogenic C-terminal 35-kD fragments due to its increased stability in the RRM1 domain. Modulation of TDP-43 stability and caspase cleavage efficiency could present an avenue for prevention and treatment of TDP-43-linked neurodegeneration.