3QKY

Crystal structure of Rhodothermus marinus BamD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of BamD. An Essential Component of the beta-Barrel Assembly Machinery of Gram Negative Bacteria

Sandoval, C.M.Baker, S.L.Jansen, K.Metzner, S.I.Sousa, M.C.

(2011) J.Mol.Biol. --: --

  • DOI: 10.1016/j.jmb.2011.03.035

  • PubMed Abstract: 
  • Folding and insertion of integral β-barrel proteins in the outer membrane (OM) is an essential process for Gram-negative bacteria that requires the β-barrel assembly machinery (BAM). Efficient OM protein (OMP) folding and insertion appears to require ...

    Folding and insertion of integral β-barrel proteins in the outer membrane (OM) is an essential process for Gram-negative bacteria that requires the β-barrel assembly machinery (BAM). Efficient OM protein (OMP) folding and insertion appears to require a consensus C-terminal signal in OMPs characterized by terminal F or W residues. The BAM complex is embedded in the OM and, in Escherichia coli, consists of the β-barrel BamA and four lipoproteins BamBCDE. BamA and BamD are broadly distributed across all species of Gram-negative bacteria, whereas the other components are present in only a subset of species. BamA and BamD are also essential for viability, suggesting that these two proteins constitute the functional core of the bacterial BAM complex. Here, we present the crystal structure of BamD from the thermophilic bacteria Rhodothermus marinus refined to 2.15 Å resolution. The protein contains five tetratricopeptide repeats (TPRs) organized into two offset tandems, each capped by a terminal helix. The N-terminal domain contains three TPRs and displays remarkable structural similarity with proteins that recognize targeting signals in extended conformations. The C-terminal domain harbors the remaining two TPRs and previously described mutations that impair binding to other BAM components map to this domain. Therefore, the structure suggests a model where the C-terminal domain provides a scaffold for interaction with BAM components, while the N-terminal domain participates in interaction with the substrates, either recognizing the C-terminal consensus sequence or binding unfolded OMP intermediates.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer membrane assembly lipoprotein YfiO
A
261Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10)Mutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamD component of the Bam β-barrel assembly machine
Find proteins for D0MFQ0 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10))
Go to UniProtKB:  D0MFQ0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 114.370α = 90.00
b = 114.370β = 90.00
c = 77.630γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-16
    Type: Atomic model