PDBsum entry 2mkn

RNA binding protein/RNA

PDB id: 2mkn

Contents

Protein chain

44 a.a.

DNA/RNA

Metals

_ZN

PDB id:

2mkn

Name:

RNA binding protein/RNA

Title:

Structural characterization of interactions between the double- stranded RNA-binding zinc finger protein jaz and dsrna

Structure:

Zinc finger protein 346. Chain: a. Fragment: unp residues 181-224. Engineered: yes. RNA (5'- r( Gp Cp Cp Gp Up Gp Gp Up Cp Up Gp Gp Up Gp Gp Cp Cp Gp G)-3'). Chain: b. Engineered: yes. RNA (5'-

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: znf346, jaz. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

NMR struc:

1 models

Authors:

P.Wright,J.Dyson,R.Burge,M.Martinez-Yamout

Key ref:

R.G.Burge et al. (2014). Structural characterization of interactions between the double-stranded RNA-binding zinc finger protein JAZ and nucleic acids. Biochemistry, 53, 1495-1510. PubMed id: 24521053 DOI: 10.1021/bi401675h

Date:

10-Feb-14 Release date: 19-Mar-14

Protein chain

Q9UL40  (ZN346_HUMAN) -  Zinc finger protein 346 from Homo sapiens

Seq: 294 a.a.

Struc: 44 a.a.

DNA/RNA chains

G-C-C-G-U-G-G-U-C-U-G-G-U-G-G-C-C-G-G 19 bases

C-C-G-G-C-C-A-C-C-A-G-A-C-C-A-C-G-G-C 19 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/bi401675h

Biochemistry 53:1495-1510 (2014)

PubMed id: 24521053

Structural characterization of interactions between the double-stranded RNA-binding zinc finger protein JAZ and nucleic acids.

R.G.Burge, M.A.Martinez-Yamout, H.J.Dyson, P.E.Wright.

ABSTRACT

The interactions of the human double-stranded RNA-binding zinc finger protein JAZ with RNA or DNA were investigated using electrophoretic mobility-shift assays, isothermal calorimetry, and nuclear magnetic resonance spectroscopy. Consistent with previous reports, JAZ has very low affinity for duplex DNA or single-stranded RNA, but it binds preferentially to double-stranded RNA (dsRNA) with no detectable sequence specificity. The affinity of JAZ for dsRNA is unaffected by local structural features such as loops, overhangs, and bulges, provided a sufficient length of reasonably well-structured A-form RNA (about 18 bp for a single zinc finger) is present. Full-length JAZ contains four Cys2His2 zinc fingers (ZF1-4) and has the highest apparent affinity for dsRNA; two-finger constructs ZF12 and ZF23 have lower affinity, and ZF34 binds even more weakly. The fourth zinc finger, ZF4, has no measurable RNA-binding affinity. Single zinc finger constructs ZF1, ZF2, and ZF3 show evidence for multiple-site binding on the minimal RNA. Fitting of quantitative NMR titration and isothermal calorimetry data to a two-site binding model gave Kd1 ∼ 10 μM and Kd2 ∼ 100 μM. Models of JAZ-RNA complexes were generated using the high-ambiguity-driven biomolecular docking (HADDOCK) program. Single zinc fingers bind to the RNA backbone without sequence specificity, forming complexes with contacts between the RNA minor groove and residues in the N-terminal β strands and between the major groove and residues in the helix-kink-helix motif. We propose that the non-sequence-specific interaction between the zinc fingers of JAZ with dsRNA is dependent only on the overall shape of the A-form RNA.