2YHC

Structure of BamD from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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:  
    2YH9, 2YH3, 2YH5, 2YH6, 2YHC

  • 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 presence of two essential components, BamA and BamD ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UPF0169 LIPOPROTEIN YFIOA225Escherichia coli BL21(DE3)Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
Explore P0AC02 
Go to UniProtKB:  P0AC02
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URE
Query on URE

Download Ideal Coordinates CCD File 
B [auth A]UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.112α = 90
b = 33.428β = 111.41
c = 57.783γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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