5XHB

Crystal structure of the full length of NisI in a lipid free form, the nisin immunity protein, from Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of NisI in a Lipid-Free Form, the Nisin Immunity Protein, from Lactococcus lactis

Jeong, J.H.Ha, S.C.

(2018) Antimicrob Agents Chemother 62

  • DOI: https://doi.org/10.1128/AAC.01966-17
  • Primary Citation of Related Structures:  
    5XHB

  • PubMed Abstract: 

    Nisin is a lantibiotic, a member of a family of polypeptides containing lanthionine with antimicrobial activity. Nisin-producing microorganisms require immunity proteins for self-protection from nisin itself. Lactococcus lactis , a microorganism that synthesizes nisin, has an integral NisFEG ABC transporter and an NisI lipoprotein that function in nisin immunity. Here, we present the crystal structure of the full length of NisI 22-C , a lipid-free form of NisI, determined at 1.9-Å resolution. As with the nuclear magnetic resonance (NMR) structures of the N- and C-terminal domains of NisI, NisI 22-C is composed of N- and C-terminal domains, both of which display a fold similar to that found in SpaI, a lipoprotein with immunity against subtilin in Bacillus subtilis The full-length structure of NisI 22-c reveals a large, deep cleft by the interdomain association, one side of which is occupied by the residues important for immunity. Opposite the cleft, a shallow groove is found where nisin-interacting residues are distributed in the periphery composed of the C-terminal negative patch. Based on a sulfate ion found in the large and deep cleft, a model of NisI in complex with a farnesyl diphosphate backbone of lipid II is proposed, suggesting a mechanism for increasing the chances of encountering nisin.


  • Organizational Affiliation

    Beamline Department, Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nisin immunity protein229Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: nisI
UniProt
Find proteins for P42708 (Lactococcus lactis subsp. lactis)
Explore P42708 
Go to UniProtKB:  P42708
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42708
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.984α = 90
b = 76.866β = 90
c = 76.667γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2017-12-27 
  • Deposition Author(s): Ha, S.C.

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Database references