Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.44 kDa 
• Atom Count: 313 
• Modelled Residue Count: 43 
• Deposited Residue Count: 43 
• Unique protein chains: 1

1OG7

Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P.

• PDB DOI: 10.2210/pdb1OG7/pdb

• Classification: ANTIBIOTIC
• Organism(s): Latilactobacillus sakei
• Expression System: Latilactobacillus sakei
• Mutation(s): No 


• Deposited: 2003-04-25 Released: 2003-09-22 
• Deposition Author(s): Uteng, M., Hauge, H.H., Markwick, P.R., Fimland, G., Mantzilas, D., Nissen-Meyer, J., Muhle-Goll, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: LEAST RESTRAIN VIOLATION AND OVERALL ENERGY 

Literature

Three-Dimensional Structure in Lipid Micelles of the Pediocin-Like Antimicrobial Peptide Sakacin P and a Sakacin P Variant that is Structurally Stabilized by an Inserted C-Terminal Disulfide Bridge

Uteng, M., Hauge, H.H., Markwick, P.R., Fimland, G., Mantzilas, D., Nissen-Meyer, J., Muhle-Goll, C.

(2003) Biochemistry 42: 11417

• PubMed: 14516192 
• DOI: 10.1021/bi034572i
• Primary Citation of Related Structures:  
  1OG7, 1OHM, 1OHN


• PubMed Abstract: 
  

The three-dimensional structures in dodecylphosphocholine (DPC) micelles and in trifluoroethanol (TFE) of the pediocin-like antimicrobial peptide sakacin P and an engineered variant of sakacin P (termed sakP[N24C+44C]) have been determined by use of nuclear magnetic resonance spectroscopy. SakP[N24C+44C] has an inserted non-native activity- and structure-stabilizing C-terminal disulfide bridge that ties the C-terminus to the middle part of the peptide. In the presence of DPC, the cationic N-terminal region (residues 1-17) of both peptides has an S-shaped conformation that is reminiscent of a three-stranded antiparallel beta-sheet and that is more pronounced when the peptide was dissolved in TFE instead of DPC. The four positively charged residues located in the N-terminal part are found pointing to the same direction. For both peptides, the N-terminal region is followed by a well-defined central amphiphilic alpha-helix (residues 18-33), and this in turn is followed by the C-terminal tail (residues 34-43 for sakacin P and 34-44 for sakP[N24C+44C]) that lacks any apparent common secondary structural motif. In the presence of DPC, the C-terminal tails in both peptides fold back onto the central alpha-helix, thereby creating a hairpin-like structure in the C-terminal halves. The lack of long-range NOEs between the beta-sheet Nu-terminal region and the hairpin-like C-terminal half indicates that there is a flexible hinge between these regions. We discuss which implications such a structural arrangement has on the interaction with the target cell membrane.

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Organizational Affiliation: 

Department of Biochemistry, University of Oslo, Oslo, Norway.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIOCIN SAKACIN P	A	43	Latilactobacillus sakei	Mutation(s): 0  Gene Names: sakP, sakR, sppA
UniProt
Find proteins for P35618 (Latilactobacillus sakei) Explore P35618  Go to UniProtKB:  P35618

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: LEAST RESTRAIN VIOLATION AND OVERALL ENERGY 
• OLDERADO: 1OG7 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-25 
• Released Date: 2003-09-22 
Deposition Author(s): Uteng, M., Hauge, H.H., Markwick, P.R., Fimland, G., Mantzilas, D., Nissen-Meyer, J., Muhle-Goll, C.

Revision History  

• Version 1.0: 2003-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance