4N75

Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural and functional analysis of the beta-barrel domain of BamA from Escherichia coli

Ni, D.C.Wang, Y.Yang, X.Zhou, H.Z.Hou, X.M.Cao, B.H.Lu, Z.X.Zhao, X.S.Yang, K.Huang, Y.H.

(2014) Faseb J. --: --

  • DOI: 10.1096/fj.13-248450

  • PubMed Abstract: 
  • In gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved component. To elucidate the mechanism of BamA-mediated OMP biog ...

    In gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved component. To elucidate the mechanism of BamA-mediated OMP biogenesis, we determined the crystal structure of the C-terminal transmembrane domain of BamA from Escherichia coli (EcBamA) at 2.6 Å resolution. The structure reveals 2 distinct features. First, a portion of the extracellular side of the β barrel is composed of 5 markedly short β strands, and the loops stemming from these β strands form a potential surface cavity, filled by a portion of the L6 loop that includes the conserved VRGF/Y motif found in the Omp85 family. Second, the 4 extracellular loops L3, L4, L6, and L7 of EcBamA form a dome over the barrel, stabilized by a salt-bridge interaction network. Functional data show that hydrophilic-to-hydrophobic mutations of the potential hydrophilic surface cavity and a single Arg547Ala point mutation that may destabilize the dome severely affect the function of EcBamA. Our structure of the EcBamA β barrel and structure-based mutagenesis studies suggest that the transmembrane β strands of OMP substrates may integrate into the outer membrane at the interface of the first and last β strands of the EcBamA barrel, whereas the soluble loops or domains may be transported out of the cell via the hydrophilic surface cavity on dislocation of the VRGF/Y motif of L6. In addition, the dome over the barrel may play an important role in maintaining the efficiency of OMP biogenesis.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Public Health, Tianjin Medical University, Tianjin, China;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane protein assembly factor BamA
A, B
385Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamA (yaeT, yzzN, yzzY)
Find proteins for P0A940 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A940
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.604 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 118.492α = 90.00
b = 159.883β = 90.00
c = 56.000γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-10-14 
  • Released Date: 2014-04-16 
  • Deposition Author(s): Ni, D.C.

Revision History 

  • Version 1.0: 2014-04-16
    Type: Initial release