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 2MII | pdb_00002mii

NMR structure of E. coli LpoB


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 750 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2MII

This is version 1.4 of the entry. See complete history. 

Literature

Outer-membrane lipoprotein LpoB spans the periplasm to stimulate the peptidoglycan synthase PBP1B.

Egan, A.J., Jean, N.L., Koumoutsi, A., Bougault, C.M., Biboy, J., Sassine, J., Solovyova, A.S., Breukink, E., Typas, A., Vollmer, W., Simorre, J.P.

(2014) Proc Natl Acad Sci U S A 111: 8197-8202

  • DOI: https://doi.org/10.1073/pnas.1400376111
  • Primary Citation Related Structures: 
    2MII

  • PubMed Abstract: 

    Bacteria surround their cytoplasmic membrane with an essential, stress-bearing peptidoglycan (PG) layer. Growing and dividing cells expand their PG layer by using membrane-anchored PG synthases, which are guided by dynamic cytoskeletal elements. In Escherichia coli, growth of the mainly single-layered PG is also regulated by outer membrane-anchored lipoproteins. The lipoprotein LpoB is required for the activation of penicillin-binding protein (PBP) 1B, which is a major, bifunctional PG synthase with glycan chain polymerizing (glycosyltransferase) and peptide cross-linking (transpeptidase) activities. Here, we report the structure of LpoB, determined by NMR spectroscopy, showing an N-terminal, 54-aa-long flexible stretch followed by a globular domain with similarity to the N-terminal domain of the prevalent periplasmic protein TolB. We have identified the interaction interface between the globular domain of LpoB and the noncatalytic UvrB domain 2 homolog domain of PBP1B and modeled the complex. Amino acid exchanges within this interface weaken the PBP1B-LpoB interaction, decrease the PBP1B stimulation in vitro, and impair its function in vivo. On the contrary, the N-terminal flexible stretch of LpoB is required to stimulate PBP1B in vivo, but is dispensable in vitro. This supports a model in which LpoB spans the periplasm to interact with PBP1B and stimulate PG synthesis.


  • Organizational Affiliation: 
    • Centre for Bacterial Cell Biology.

Macromolecule Content 

  • Total Structure Weight: 20.77 kDa 
  • Atom Count: 1,456 
  • Modeled Residue Count: 197 
  • Deposited Residue Count: 197 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Penicillin-binding protein activator LpoB197Escherichia coli str. K-12 substr. DH10BMutation(s): 0 
Gene Names: ycfM, lpoB, ECDH10B_1177
UniProt
Find proteins for P0AB38 (Escherichia coli (strain K12))
Explore P0AB38 
Go to UniProtKB:  P0AB38
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AB38
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 750 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references
  • Version 1.3: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references