3TGO

Crystal structure of the E. coli BamCD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the beta-barrel assembly machinery BamCD protein complex

Kim, K.H.Aulakh, S.Paetzel, M.

(2011) J.Biol.Chem. 286: 39116-39121

  • DOI: 10.1074/jbc.M111.298166

  • PubMed Abstract: 
  • The β-barrel assembly machinery (BAM) complex of Escherichia coli is a multiprotein machine that catalyzes the essential process of assembling outer membrane proteins. The BAM complex consists of five proteins: one membrane protein, BamA, and four li ...

    The β-barrel assembly machinery (BAM) complex of Escherichia coli is a multiprotein machine that catalyzes the essential process of assembling outer membrane proteins. The BAM complex consists of five proteins: one membrane protein, BamA, and four lipoproteins, BamB, BamC, BamD, and BamE. Here, we report the first crystal structure of a Bam lipoprotein complex: the essential lipoprotein BamD in complex with the N-terminal half of BamC (BamC(UN) (Asp(28)-Ala(217)), a 73-residue-long unstructured region followed by the N-terminal domain). The BamCD complex is stabilized predominantly by various hydrogen bonds and salt bridges formed between BamD and the N-terminal unstructured region of BamC. Sequence and molecular surface analyses revealed that many of the conserved residues in both proteins are found at the BamC-BamD interface. A series of truncation mutagenesis and analytical gel filtration chromatography experiments confirmed that the unstructured region of BamC is essential for stabilizing the BamCD complex structure. The unstructured N terminus of BamC interacts with the proposed substrate-binding pocket of BamD, suggesting that this region of BamC may play a regulatory role in outer membrane protein biogenesis.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UPF0169 lipoprotein yfiO
A, B
229Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamD (yfiO)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamCD complex of the Bam β-barrel assembly machine
Find proteins for P0AC02 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AC02
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein 34
C, D
323Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamC (dapX, nlpB)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamCD complex of the Bam β-barrel assembly machine
Find proteins for P0A903 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A903
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

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D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, B, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.177 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 73.780α = 90.00
b = 133.380β = 100.15
c = 144.992γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-11-16
    Type: Database references