Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1.83 kDa 
• Atom Count: 125 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique protein chains: 1

1MQZ

NMR solution structure of type-B lantibiotics mersacidin bound to lipid II in DPC micelles

• PDB DOI: 10.2210/pdb1MQZ/pdb
• BMRB: 5580

• Classification: ANTIBIOTIC
• Organism(s): Bacillus sp. HIL-Y85/54728
• Mutation(s): No 


• Deposited: 2002-09-17 Released: 2003-03-11 
• Deposition Author(s): Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 17 
• Selection Criteria: structures with the lowest energy 

Literature

NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles. Conformational Changes are a Key to Antimicrobial Activity

Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., De Kruijff, B., Kaptein, R., Van Nuland, N.A., Bonvin, A.M.

(2003) J Biol Chem 278: 13110

• PubMed: 12562773 
• DOI: 10.1074/jbc.M211144200
• Primary Citation of Related Structures:  
  1MQX, 1MQY, 1MQZ


• PubMed Abstract: 
  

Mersacidin belongs to the type B lantibiotics (lanthionine-containing antibiotics) that contain post-translationally modified amino acids and cyclic ring structures. It targets the cell wall precursor lipid II and thereby inhibits cell wall synthesis. In light of the emerging antibiotics resistance problem, the understanding of the antibacterial activity on a structural basis provides a key to circumvent this issue. Here we present solution NMR studies of mersacidin-lipid II interaction in dodecylphosphocholine (DPC) micelles. Distinct solution structures of mersacidin were determined in three different states: in water/methanol solution and in DPC micelles with and without lipid II. The structures in various sample conditions reveal remarkable conformational changes in which the junction between Ala-12 and Abu-13 (where Abu is aminobutyric acid) effectively serves as the hinge for the opening and closure of the ring structures. The DPC micelle-bound form resembles the previously determined NMR and x-ray crystal structures of mersacidin in pure methanol but substantially deviates from the other two states in our current report. The structural changes delineate the large chemical shift perturbations observed during the course of a two-step (15)N-(1)H heteronuclear single quantum coherence titration. They also modulate the surface charge distribution of mersacidin suggesting that electrostatics play a central role in the mersacidin-lipid II interaction. The observed conformational adaptability of mersacidin might be a general feature of lipid II-interacting antibiotics/peptides.

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Organizational Affiliation: 

NMR Department, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LANTIBIOTIC MERSACIDIN	A	20	Bacillus sp. HIL-Y85/54728	Mutation(s): 0  Gene Names: mrsA
UniProt
Find proteins for P43683 (Bacillus sp. (strain HIL-Y85/54728)) Explore P43683  Go to UniProtKB:  P43683

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000199	A	Mersacidin	Oligopeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 17 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 1MQZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-17 
• Released Date: 2003-03-11 
Deposition Author(s): Hsu, S.-T., Breukink, E., Bierbaum, G., Sahl, H.-G., de Kruijff, B., Kaptein, R., van Nuland, N.A., Bonvin, A.M.

Revision History  

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2009-02-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2011-07-27
  Changes: Other
• Version 1.4: 2012-12-12
  Changes: Other
• Version 1.5: 2018-08-08
  Changes: Data collection, Database references, Derived calculations, Experimental preparation