Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5

Komal Soni; Santiago Martínez-Lumbreras; Michael Sattler

doi:10.1016/j.jmb.2020.05.012

Conformational Dynamics from Ambiguous Zinc Coordination in the RanBP2-Type Zinc Finger of RBM5

J Mol Biol. 2020 Jun 26;432(14):4127-4138. doi: 10.1016/j.jmb.2020.05.012. Epub 2020 May 22.

Authors

Komal Soni¹, Santiago Martínez-Lumbreras¹, Michael Sattler²

Affiliations

¹ Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Bavarian NMR Center and Biomolecular NMR, Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
² Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich at Bavarian NMR Center and Biomolecular NMR, Department Chemie, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany. Electronic address: sattler@helmholtz-muenchen.de.

PMID: 32450081
DOI: 10.1016/j.jmb.2020.05.012

Abstract

The multi-domain RNA binding protein RBM5 is a molecular signature of metastasis. RBM5 regulates alternative splicing of apoptotic genes including the cell death receptor Fas and the initiator Caspase-2. The RBM5 RanBP2-type zinc finger (Zf1) is known to specifically recognize single-stranded RNAs with high affinity. Here, we study the structure and conformational dynamics of the Zf1 zinc finger of human RBM5 using NMR. We show that the presence of a non-canonical cysteine in Zf1 kinetically destabilizes the protein. Metal-exchange kinetics show that mutation of the cysteine establishes high-affinity coordination of the zinc. Our data indicate that selection of such a structurally destabilizing mutation during the course of evolution could present an opportunity for functional adaptation of the protein.

Keywords: NMR; RBM5; RanBP2 Zinc finger; metal-exchange kinetics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing / genetics
Amino Acid Sequence / genetics
Apoptosis / genetics
Caspase 2 / genetics
Cell Cycle Proteins / chemistry
Cell Cycle Proteins / genetics
Cell Cycle Proteins / ultrastructure*
DNA-Binding Proteins / chemistry
DNA-Binding Proteins / genetics
DNA-Binding Proteins / ultrastructure*
Humans
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Chaperones / chemistry
Molecular Chaperones / genetics
Molecular Chaperones / ultrastructure*
Nuclear Pore Complex Proteins / chemistry
Nuclear Pore Complex Proteins / genetics
Nuclear Pore Complex Proteins / ultrastructure*
Protein Binding / genetics
Protein Conformation
RNA-Binding Proteins / chemistry
RNA-Binding Proteins / genetics
RNA-Binding Proteins / ultrastructure*
Transcription Factors / genetics
Tumor Suppressor Proteins / chemistry
Tumor Suppressor Proteins / genetics
Tumor Suppressor Proteins / ultrastructure*
Zinc / chemistry
Zinc Fingers / genetics*

Substances

Cell Cycle Proteins
DNA-Binding Proteins
Molecular Chaperones
Nuclear Pore Complex Proteins
RBM5 protein, human
RNA-Binding Proteins
Transcription Factors
Tumor Suppressor Proteins
ran-binding protein 2
Caspase 2
Zinc