6XN9

Solution NMR structure of recifin, a cysteine-rich tyrosyl-DNA Phosphodiesterase I modulatory peptide from the marine sponge Axinella sp.

Summary for 6XN9

• Entry DOI: 10.2210/pdb6xn9/pdb
• NMR Information: BMRB: 30767
• Descriptor: Recifin modulatory peptide (1 entity in total)
• Functional Keywords: cystine-rich peptide, protein knot, tyrosyl-dna phosphodiesterase i inhibitor, marine natural product, toxin
• Biological source: Axinella sp. 1 TF-2017
• Total number of polymer chains: 1
• Total formula weight: 4924.44

Authors

Schroeder, C.I.,Rosengren, K.J.,O'Keefe, B.R. (deposition date: 2020-07-02, release date: 2021-02-10, Last modification date: 2024-11-06)

Primary citation

Krumpe, L.R.H.,Wilson, B.A.P.,Marchand, C.,Sunassee, S.N.,Bermingham, A.,Wang, W.,Price, E.,Guszczynski, T.,Kelley, J.A.,Gustafson, K.R.,Pommier, Y.,Rosengren, K.J.,Schroeder, C.I.,O'Keefe, B.R.
Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I.
J.Am.Chem.Soc., 142:21178-21188, 2020

PubMed Abstract: Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a molecular target for the sensitization of cancer cells to the FDA-approved topoisomerase inhibitors topotecan and irinotecan. High-throughput screening of natural product extract and fraction libraries for inhibitors of TDP1 activity resulted in the discovery of a new class of knotted cyclic peptides from the marine sponge sp. Bioassay-guided fractionation of the source extract resulted in the isolation of the active component which was determined to be an unprecedented 42-residue cysteine-rich peptide named recifin A. The native NMR structure revealed a novel fold comprising a four strand antiparallel β-sheet and two helical turns stabilized by a complex disulfide bond network that creates an embedded ring around one of the strands. The resulting structure, which we have termed the Tyr-lock peptide family, is stabilized by a tyrosine residue locked into three-dimensional space. Recifin A inhibited the cleavage of phosphodiester bonds by TDP1 in a FRET assay with an IC of 190 nM. Enzyme kinetics studies revealed that recifin A can specifically modulate the enzymatic activity of full-length TDP1 while not affecting the activity of a truncated catalytic domain of TDP1 lacking the N-terminal regulatory domain (Δ1-147), suggesting an allosteric binding site for recifin A on the regulatory domain of TDP1. Recifin A represents both the first of a unique structural class of knotted disulfide-rich peptides and defines a previously unseen mechanism of TDP1 inhibition that could be productively exploited for potential anticancer applications.

PubMed: 33263997
DOI: 10.1021/jacs.0c10418

Experimental method

SOLUTION NMR