7F32 | pdb_00007f32

Ny-Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases

• PDB DOI: https://doi.org/10.2210/pdb7F32/pdb
• BMRB: 36425

• Classification: METAL BINDING PROTEIN
• Organism(s): Macaca mulatta
• Mutation(s): No 


• Deposited: 2021-06-15 Released: 2022-09-07 
• Deposition Author(s): Xia, Y., Liu, C.F.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 9 
• Selection Criteria: structures with acceptable covalent geometry 

Literature

N gamma-Hydroxyasparagine: A Multifunctional Unnatural Amino Acid That is a Good P1 Substrate of Asparaginyl Peptide Ligases.

Xia, Y., To, J., Chan, N.Y., Hu, S., Liew, H.T., Balamkundu, S., Zhang, X., Lescar, J., Bhattacharjya, S., Tam, J.P., Liu, C.F.

(2021) Angew Chem Int Ed Engl 60: 22207-22211

• PubMed: 34396662 
• DOI: https://doi.org/10.1002/anie.202108125
• Primary Citation Related Structures: 
  7F32


• PubMed Abstract: 
  

  Peptidyl asparaginyl ligases (PALs) are powerful tools for peptide macrocyclization. Herein, we report that a derivative of Asn, namely N ^γ -hydroxyasparagine or Asn(OH), is an unnatural P1 substrate of PALs. By Asn(OH)-mediated cyclization, we prepared cyclic peptides as new matrix metalloproteinase 2 (MMP2) inhibitors displaying the hydroxamic acid moiety of Asn(OH) as the key pharmacophore. The most potent cyclic peptide (K _i =2.8±0.5 nM) was built on the hyperstable tetracyclic scaffold of rhesus theta defensin-1. The Asn(OH) residue in the cyclized peptides can also be readily oxidized to Asp. By this approach, we synthesized several bioactive Asp-containing cyclic peptides (MCoTI-II, kB2, SFTI, and integrin-targeting RGD peptides) that are otherwise difficult targets for PAL-catalyzed cyclization owing to unfavorable kinetics of the P1-Asp substrates. This study demonstrates that substrate engineering is a useful strategy to expand the application of PAL ligation in the synthesis of therapeutic cyclic peptides.

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Organizational Affiliation: 
• School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
Singapore-MIT Alliance for Research and Technology, Singapore, 138602, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.07 kDa 
• Atom Count: 137 
• Modeled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SYCNCLCRRGVCRCICTI	A	18	Macaca mulatta	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 9 
• Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Xia, Y., Liu, C.F.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE2016-T3-1-003

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary