4MZD

High resolution crystal structure of the nisin leader peptidase NisP from Lactococcus lactis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity.

Xu, Y.Li, X.Li, R.Li, S.Ni, H.Wang, H.Xu, H.Zhou, W.Saris, P.E.Yang, W.Qiao, M.Rao, Z.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1499-1505

  • DOI: 10.1107/S1399004714004234
  • Primary Citation of Related Structures:  
    4MZD

  • PubMed Abstract: 
  • Nisin is a widely used antibacterial lantibiotic polypeptide produced by Lactococcus lactis. NisP belongs to the subtilase family and functions in the last step of nisin maturation as the leader-peptide peptidase. Deletion of the nisP gene in LAC71 r ...

    Nisin is a widely used antibacterial lantibiotic polypeptide produced by Lactococcus lactis. NisP belongs to the subtilase family and functions in the last step of nisin maturation as the leader-peptide peptidase. Deletion of the nisP gene in LAC71 results in the production of a non-active precursor peptide with the leader peptide unremoved. Here, the 1.1 Å resolution crystal structure of NisP is reported. The structure shows similarity to other subtilases, which can bind varying numbers of Ca atoms. However, no calcium was found in this NisP structure, and the predicted calcium-chelating residues were placed so as to not allow NisP to bind a calcium ion in this conformation. Interestingly, a short peptide corresponding to its own 635-647 sequence was found to bind to the active site of NisP. Biochemical assays and native mass-spectrometric analysis confirmed that NisP possesses an auto-cleavage site between residues Arg647 and Ser648. Further, it was shown that NisP mutated at the auto-cleavage site (R647P/S648P) had full catalytic activity for nisin leader-peptide cleavage, although the C-terminal region of NisP was no longer cleaved. Expressing this mutant in L. lactis LAC71 did not affect the production of nisin but did decrease the proliferation rate of the bacteria, suggesting the biological significance of the C-terminal auto-cleavage of NisP.


    Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nisin leader peptide-processing serine protease NisPA488Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: nisP
EC: 3.4.21
Find proteins for Q07596 (Lactococcus lactis subsp. lactis)
Explore Q07596 
Go to UniProtKB:  Q07596
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.89α = 90
b = 44.973β = 106.82
c = 74.651γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Structure summary
  • Version 1.2: 2014-09-24
    Changes: Database references