Mechanism of β-actin mRNA Recognition by ZBP1.
Zipcode binding protein 1 (ZBP1) is an oncofetal RNA-binding protein that mediates the transport and local translation of β-actin mRNA by the KH3-KH4 di-domain, which is essential for neuronal development. The high-resolution structures of KH3-KH4 with their respective target sequences show that KH4 recognizes a non-canonical GGA sequence via an enlarged and dynamic hydrophobic groove, whereas KH3 binding to a core CA sequence occurs with low specificity. A data-informed kinetic simulation of the two-step binding reaction reveals that the overall reaction is driven by the second binding event and that the moderate affinities of the individual interactions favor RNA looping. Furthermore, the concentration of ZBP1, but not of the target RNA, modulates the interaction, which explains the functional significance of enhanced ZBP1 expression during embryonic development.
Macromolecular Structure Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
Giuseppe
G
Nicastro
At the former MRC National Institute for Medical Research, Mill Hill, London.
Adela M
AM
Candel
Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany.
Michael
M
Uhl
MRC Biomedical NMR Centre, The Francis Crick Institute, London NW1 1AT, UK.
Alain
A
Oregioni
Mycobacterial Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK.
David
D
Hollingworth
Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany; Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79110 Freiburg, Germany.
Rolf
R
Backofen
Structural Biology Science Technology Platform, The Francis Crick Institute, London NW1 1AT, UK.
Stephen R
SR
Martin
Institute of Structural and Molecular Biology, University College London, London WC1E 6XA, UK; The Francis Crick Institute, London NW1 1AT, UK. Electronic address: a.ramos@ucl.ac.uk.
Andres
A
Ramos
D000199:Actins / Q000378:metabolism*; D000595:Amino Acid Sequence; D000818:Animals; D030161:Avian Proteins / Q000378:metabolism*; D002645:Chickens / Q000378:metabolism; D047108:Embryonic Development / Q000502:physiology; D012313:RNA / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*
D000199:Actins; D030161:Avian Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; C498636:ZBP1 protein, Gallus gallus; D012313:RNA
IMP1; NMR; ZBP1; binding mechanism; mRNA local translation; neuronal development; neuronal mRNA granules; protein-RNA interactions