Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.09 kDa 
• Atom Count: 1647 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique protein chains: 1

2MH5

Structure and NMR assignments of lantibiotic NAI-107 in DPC micelles

• PDB DOI: 10.2210/pdb2MH5/pdb
• BMRB: 19619

• Classification: ANTIBIOTIC
• Organism(s): Microbispora sp. 107891
• Mutation(s): No 


• Deposited: 2013-11-18 Released: 2014-03-05 
• Deposition Author(s): Munch, D., Muller, A., Schneider, T., Kohl, B., Wenzel, M., Bandow, J., Maffioli, S., Sosio, M., Donadio, S., Wimmer, R., Sahl, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

The Lantibiotic NAI-107 Binds to Bactoprenol-bound Cell Wall Precursors and Impairs Membrane Functions.

Munch, D., Muller, A., Schneider, T., Kohl, B., Wenzel, M., Bandow, J.E., Maffioli, S., Sosio, M., Donadio, S., Wimmer, R., Sahl, H.G.

(2014) J Biol Chem 289: 12063-12076

• PubMed: 24627484 
• DOI: 10.1074/jbc.M113.537449
• Primary Citation of Related Structures:  
  2MH5


• PubMed Abstract: 
  

The lantibiotic NAI-107 is active against Gram-positive bacteria including vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. To identify the molecular basis of its potency, we studied the mode of action in a series of whole cell and in vitro assays and analyzed structural features by nuclear magnetic resonance (NMR). The lantibiotic efficiently interfered with late stages of cell wall biosynthesis and induced accumulation of the soluble peptidoglycan precursor UDP-N-acetylmuramic acid-pentapeptide (UDP-MurNAc-pentapeptide) in the cytoplasm. Using membrane preparations and a complete cascade of purified, recombinant late stage peptidoglycan biosynthetic enzymes (MraY, MurG, FemX, PBP2) and their respective purified substrates, we showed that NAI-107 forms complexes with bactoprenol-pyrophosphate-coupled precursors of the bacterial cell wall. Titration experiments indicate that first a 1:1 stoichiometric complex occurs, which then transforms into a 2:1 (peptide: lipid II) complex, when excess peptide is added. Furthermore, lipid II and related molecules obviously could not serve as anchor molecules for the formation of defined and stable nisin-like pores, however, slow membrane depolarization was observed after NAI-107 treatment, which could contribute to killing of the bacterial cell.

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Organizational Affiliation: 

From the Institute of Medical Microbiology, Immunology and Parasitology, Pharmaceutical Microbiology Section, University of Bonn, 53115 Bonn, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lantibiotic 107891	A	24	Microbispora sp. 107891	Mutation(s): 0
UniProt
Find proteins for P85065 (Microbispora sp. (strain 107891)) Explore P85065  Go to UniProtKB:  P85065

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPV	AA [auth A], AB [auth A], B [auth A], BA [auth A], BB [auth A], C [auth A], CA [auth A], CB [auth A], D [auth A], DA [auth A], DB [auth A], E [auth A], EA [auth A], EB [auth A], F [auth A], FA [auth A], FB [auth A], G [auth A], GA [auth A], GB [auth A], H [auth A], HA [auth A], HB [auth A], I [auth A], IA [auth A], IB [auth A], J [auth A], JA [auth A], JB [auth A], K [auth A], KA [auth A], KB [auth A], L [auth A], LA [auth A], LB [auth A], M [auth A], MA [auth A], MB [auth A], N [auth A], NA [auth A], NB [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], RA [auth A], S [auth A], SA [auth A], T [auth A], TA [auth A], U [auth A], UA [auth A], V [auth A], VA [auth A], W [auth A], WA [auth A], X [auth A], XA [auth A], Y [auth A], YA [auth A], Z [auth A], ZA [auth A]	dodecyl 2-(trimethylammonio)ethyl phosphate C17 H38 N O4 P QBHFVMDLPTZDOI-UHFFFAOYSA-N

Modified Residues  4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5CW	A	L-PEPTIDE LINKING	C11 H11 Cl N2 O2		TRP
DBU	A	PEPTIDE LINKING	C4 H7 N O2		THR
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001219	A	Lantibiotic 107891	Oligopeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 80 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 
• OLDERADO: 2MH5 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-11-18 
• Released Date: 2014-03-05 
Deposition Author(s): Munch, D., Muller, A., Schneider, T., Kohl, B., Wenzel, M., Bandow, J., Maffioli, S., Sosio, M., Donadio, S., Wimmer, R., Sahl, H.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-04-02
  Changes: Database references
• Version 1.2: 2014-05-14
  Changes: Database references