4Y68 | pdb_00004y68

Structure of a lipoprotein from Streptococcus agalactiae

• PDB DOI: https://doi.org/10.2210/pdb4Y68/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus agalactiae 515
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-02-12 Released: 2016-01-20 
• Deposition Author(s): Khosa, S., Hoeppner, A., Smits, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae.

Khosa, S., Frieg, B., Mulnaes, D., Kleinschrodt, D., Hoeppner, A., Gohlke, H., Smits, S.H.

(2016) Sci Rep 6: 18679-18679

• PubMed: 26727488 
• DOI: https://doi.org/10.1038/srep18679
• Primary Citation Related Structures: 
  4Y68


• PubMed Abstract: 
  

  Lantibiotics are potent antimicrobial peptides. Nisin is the most prominent member and contains five crucial lanthionine rings. Some clinically relevant bacteria express membrane-associated resistance proteins that proteolytically inactivate nisin. However, substrate recognition and specificity of these proteins is unknown. Here, we report the first three-dimensional structure of a nisin resistance protein from Streptococcus agalactiae (SaNSR) at 2.2 Å resolution. It contains an N-terminal helical bundle, and protease cap and core domains. The latter harbors the highly conserved TASSAEM region, which lies in a hydrophobic tunnel formed by all domains. By integrative modeling, mutagenesis studies, and genetic engineering of nisin variants, a model of the SaNSR/nisin complex is generated, revealing that SaNSR recognizes the last C-terminally located lanthionine ring of nisin. This determines the substrate specificity of SaNSR and ensures the exact coordination of the nisin cleavage site at the TASSAEM region.

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Organizational Affiliation: 
• Institute of Biochemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
Protein Production Facility, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
Crystal and X-ray Facility, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 142.61 kDa 
• Atom Count: 9,588 
• Modeled Residue Count: 1,147 
• Deposited Residue Count: 1,248 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative nisin-resistance protein	A [auth C], B [auth A], C [auth B], D	312	Streptococcus agalactiae 515	Mutation(s): 0  Gene Names: SAL_1042
UniProt
Find proteins for A0A140UHB6 (Streptococcus agalactiae 515) Explore A0A140UHB6  Go to UniProtKB:  A0A140UHB6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	E [auth C], F [auth C], G [auth A], H [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.81	α = 90
b = 137.24	β = 90
c = 164	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Khosa, S., Hoeppner, A., Smits, S.H.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references