4MZD

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

Summary for 4MZD

• Entry DOI: 10.2210/pdb4mzd/pdb
• Descriptor: Nisin leader peptide-processing serine protease NisP (2 entities in total)
• Functional Keywords: alpha and beta proteins, subtilisin-like, serine protease, hydrolase
• Biological source: Lactococcus lactis subsp. lactis
• Total number of polymer chains: 1
• Total formula weight: 53949.65

Authors

Rao, Z.H.,Xu, Y.Y.,Li, X.,Yang, W. (deposition date: 2013-09-30, release date: 2014-06-11, Last modification date: 2024-02-28)

Primary citation

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.
Structure of the nisin leader peptidase NisP revealing a C-terminal autocleavage activity.
Acta Crystallogr.,Sect.D, 70:1499-1505, 2014

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 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.

PubMed: 24914961
DOI: 10.1107/S1399004714004234

Experimental method

X-RAY DIFFRACTION (1.1 Å)