8V2V | pdb_00008v2v

Solution NMR structure of recifin A [Y6F]

• PDB DOI: https://doi.org/10.2210/pdb8V2V/pdb
• BMRB: 31130

• Classification: TOXIN
• Organism(s): Axinella sp. 1 TF-2017
• Mutation(s): No 


• Deposited: 2023-11-23 Released: 2024-09-25 
• Deposition Author(s): Payne, C.D., Schroeder, C.I., Rosengren, K.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with acceptable covalent geometry 

Literature

Picking the tyrosine-lock: chemical synthesis of the tyrosyl-DNA phosphodiesterase I inhibitor recifin A and analogues.

Smallwood, T.B., Krumpe, L.R.H., Payne, C.D., Klein, V.G., O'Keefe, B.R., Clark, R.J., Schroeder, C.I., Rosengren, K.J.

(2024) Chem Sci 15: 13227-13233

• PubMed: 39183914 
• DOI: https://doi.org/10.1039/d4sc01976h
• Primary Citation of Related Structures:  
  8V2V


• PubMed Abstract: 
  

  The peptide recifin A is the inaugural member of the structurally intriguing new fold referred to as a tyrosine-lock. Its central four stranded β-sheet is stabilized by a unique arrangement in which three disulfide bonds and their interconnecting backbone form a ring that wraps around one of the strands, resulting in a Tyr side chain being buried in the molecular core. Here we aimed to establish a synthetic route to this complex class of natural products. Full length recifin A was successfully generated through native chemical ligation chemistry joining two 21 amino acid residue fragments. Surprisingly, reduced linear recifin A readily adopts the correct, topologically-complex fold via random oxidation of the cysteines, suggesting it is highly energetically favored. Utilizing our synthetic strategy, we generated five recifin A analogues to investigate the structural role of the central Tyr residue and provide the first insights into the structure activity relationship of recifin A towards its cancer target tyrosyl-DNA phosphodiesterase I.

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Organizational Affiliation: 
• The University of Queensland, School of Biomedical Sciences Brisbane QLD 4072 Australia [e-mail] [e-mail].
Molecular Targets Program, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA.
Chemical Biology Laboratory, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA.
Natural Products Branch, Centre for Cancer Research, National Cancer Institute, National Institute of Health Frederick MD 21702 USA.
Peptide Therapeutics, Genentech Inc 1 DNA Way South San Francisco CA 94080 USA [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 4.93 kDa 
• Atom Count: 343 
• Modeled Residue Count: 41 
• Deposited Residue Count: 41 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recifin A	A	41	Axinella sp. 1 TF-2017	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCA	B [auth A]	PYROGLUTAMIC ACID C5 H7 N O3 ODHCTXKNWHHXJC-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Payne, C.D., Schroeder, C.I., Rosengren, K.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release