2K1I | pdb_00002k1i

Synthesis, Structure and Activities of an Oral Mucosal Alpha-Defensin from Rhesus Macaque

• PDB DOI: https://doi.org/10.2210/pdb2K1I/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Macaca mulatta
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2008-03-05 Released: 2008-10-28 
• Deposition Author(s): Vasudevan, S.V., Yuan, J., Osapay, G., Tran, P., Tai, K., Selsted, M., Cocco, M.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations, strutures with the lowest energy 

Literature

Synthesis, structure, and activities of an oral mucosal alpha-defensin from rhesus macaque.

Vasudevan, S., Yuan, J., Osapay, G., Tran, P., Tai, K., Liang, W., Kumar, V., Selsted, M.E., Cocco, M.J.

(2008) J Biological Chem 283: 35869-35877

• PubMed: 18930922 
• DOI: https://doi.org/10.1074/jbc.M806915200
• Primary Citation Related Structures: 
  2K1I


• PubMed Abstract: 
  

  The oral cavity is an environment challenged by a large variety of pathogens. Consequently, the antimicrobial peptides expressed in that environment are interesting as they evolved to defend against a broad spectrum of bacteria and fungi. Here we report the discovery of new alpha-defensins from rhesus macaque oral mucosa and determine the first alpha-defensin structure from that species. The new peptides were identified by sequencing of reverse transcriptase-PCR products obtained from oral mucosal tissues, disclosing three mucosal alpha-defensins, termed rhesus macaque oral alpha-defensins (ROADs). The peptide corresponding to fully processed ROAD-1 was synthesized, subjected to folding/oxidation conditions, and purified. ROAD-1 was active against Staphylococcus aureus, Escherichia coli, and Candida albicans in a concentration-dependent manner. We determined the structure of ROAD-1 using NMR spectroscopy and find that the synthetic peptide adopts the canonical disulfide pairing and alpha-defensin fold. The antimicrobial mechanism of defensins has been correlated with their ability to disrupt and permeabilize the cell envelope, activities that depend on the surface features of the folded peptide. Although ROAD-1 maintains the defensin fold, the oral defensin displays distinct surface features when compared with other alpha-defensin structures.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.75 kDa 
• Atom Count: 256 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucosal Alpha-Defensin	A	32	Macaca mulatta	Mutation(s): 0  Gene Names: ROAD-1 Membrane Entity: Yes
UniProt
Find proteins for B5AKV3 (Macaca mulatta) Explore B5AKV3  Go to UniProtKB:  B5AKV3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 60 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations, strutures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-28 
Deposition Author(s): Vasudevan, S.V., Yuan, J., Osapay, G., Tran, P., Tai, K., Selsted, M., Cocco, M.J.

Revision History  

• Version 1.0: 2008-10-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-06-19
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary