6YN0

Structure of E. coli PBP1b with a FtsN peptide activating transglycosylase activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The bacterial cell division protein fragment E FtsN binds to and activates the major peptidoglycan synthase PBP1b.

Boes, A.Kerff, F.Herman, R.Touze, T.Breukink, E.Terrak, M.

(2020) J Biol Chem 295: 18256-18265

  • DOI: https://doi.org/10.1074/jbc.RA120.015951
  • Primary Citation of Related Structures:  
    6YN0

  • PubMed Abstract: 

    Peptidoglycan (PG) is an essential constituent of the bacterial cell wall. During cell division, the machinery responsible for PG synthesis localizes mid-cell, at the septum, under the control of a multiprotein complex called the divisome. In Escherichia coli , septal PG synthesis and cell constriction rely on the accumulation of FtsN at the division site. Interestingly, a short sequence of FtsN (Leu 75 -Gln 93 , known as E FtsN) was shown to be essential and sufficient for its functioning in vivo , but what exactly this sequence is doing remained unknown. Here, we show that E FtsN binds specifically to the major PG synthase PBP1b and is sufficient to stimulate its biosynthetic glycosyltransferase (GTase) activity. We also report the crystal structure of PBP1b in complex with E FtsN, which demonstrates that E FtsN binds at the junction between the GTase and UB2H domains of PBP1b. Interestingly, mutations to two residues (R141A/R397A) within the E FtsN-binding pocket reduced the activation of PBP1b by FtsN but not by the lipoprotein LpoB. This mutant was unable to rescue the Δ ponB - ponA ts strain, which lacks PBP1b and has a thermosensitive PBP1a, at nonpermissive temperature and induced a mild cell-chaining phenotype and cell lysis. Altogether, the results show that E FtsN interacts with PBP1b and that this interaction plays a role in the activation of its GTase activity by FtsN, which may contribute to the overall septal PG synthesis and regulation during cell division.


  • Organizational Affiliation

    InBioS-Centre d'Ingénierie des Protéines, Liège University, Liège, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Penicillin-binding protein 1B747Escherichia coli K-12Mutation(s): 0 
Gene Names: mrcBpbpFponBb0149JW0145
EC: 2.4.1.129 (PDB Primary Data), 3.4.16.4 (PDB Primary Data), 2.4.99.28 (UniProt)
UniProt
Find proteins for P02919 (Escherichia coli (strain K12))
Explore P02919 
Go to UniProtKB:  P02919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02919
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsN19Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P29131 (Escherichia coli (strain K12))
Explore P29131 
Go to UniProtKB:  P29131
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29131
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M0E
Query on M0E

Download Ideal Coordinates CCD File 
C [auth A]MOENOMYCIN
C69 H106 N5 O34 P
NXPRJQIAIORCGO-ZLPAOQQDSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.143α = 90
b = 283.021β = 90
c = 62.693γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references
  • Version 1.2: 2021-01-06
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description