2MKN

Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and dsRNA

Summary for 2MKN

• Entry DOI: 10.2210/pdb2mkn/pdb
• Related: 2MKD
• NMR Information: BMRB: 17679
• Descriptor: Zinc finger protein 346, RNA (5'-R(*GP*CP*CP*GP*UP*GP*GP*UP*CP*UP*GP*GP*UP*GP*GP*CP*CP*GP*G)-3'), RNA (5'-R(P*CP*CP*GP*GP*CP*CP*AP*CP*CP*AP*GP*AP*CP*CP*AP*CP*GP*GP*C)-3'), ... (4 entities in total)
• Functional Keywords: zinc finger, dsrna-binding, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus, nucleolus : Q9UL40
• Total number of polymer chains: 3
• Total formula weight: 19302.94

Authors

Wright, P.,Dyson, J.,Burge, R.,Martinez-Yamout, M. (deposition date: 2014-02-10, release date: 2014-03-19, Last modification date: 2024-05-01)

Primary citation

Burge, R.G.,Martinez-Yamout, M.A.,Dyson, H.J.,Wright, P.E.
Structural Characterization of Interactions between the Double-Stranded RNA-Binding Zinc Finger Protein JAZ and Nucleic Acids.
Biochemistry, 53:1495-1510, 2014

PubMed 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.

PubMed: 24521053
DOI: 10.1021/bi401675h

Experimental method

SOLUTION NMR