2YHC

Structure of BamD from E. coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.

Albrecht, R., Zeth, K.

(2011) J.Biol.Chem. 286: 27792

  • DOI: 10.1074/jbc.M111.238931
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • In Escherichia coli, a multicomponent BAM (β-barrel assembly machinery) complex is responsible for recognition and assembly of outer membrane β-barrel proteins. The functionality of BAM in protein biogenesis is mainly orchestrated through the presenc ...

    In Escherichia coli, a multicomponent BAM (β-barrel assembly machinery) complex is responsible for recognition and assembly of outer membrane β-barrel proteins. The functionality of BAM in protein biogenesis is mainly orchestrated through the presence of two essential components, BamA and BamD. Here, we present crystal structures of four lipoproteins (BamB-E). Monomeric BamB and BamD proteins display scaffold architectures typically implied in transient protein interactions. BamB is a β-propeller protein comprising eight WD40 repeats. BamD shows an elongated fold on the basis of five tetratricopeptide repeats, three of which form the scaffold for protein recognition. The rod-shaped BamC protein has evolved through the gene duplication of two conserved domains known to mediate protein interactions in structurally related complexes. By contrast, the dimeric BamE is formed through a domain swap and indicates fold similarity to the β-lactamase inhibitor protein family, possibly integrating cell wall stability in BAM function. Structural and biochemical data show evidence for the specific recognition of amphipathic sequences through the tetratricopeptide repeat architecture of BamD. Collectively, our data advance the understanding of the BAM complex and highlight the functional importance of BamD in amphipathic outer membrane β-barrel protein motif recognition and protein delivery.

    Organizational Affiliation: 

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen 72076, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UPF0169 LIPOPROTEIN YFIO
A
225Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamD (yfiO)
Membrane protein
mpstruc		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 P0AC02 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC02
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URE
Query on URE
Download SDF File 
Download CCD File 
A
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.112α = 90.00
b = 33.428β = 111.41
c = 57.783γ = 90.00
Software Package:
Software NamePurpose
DMphasing
REFMACrefinement
SHARPphasing
XDSdata reduction
XDSdata scaling
BUCCANEERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2011-04-28 
  • Released Date: 2011-06-01 
  • Deposition Author(s): Zeth, K., Albrecht, R.

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-08-10
    Type: Database references, Version format compliance