6AIT

Crystal structure of E. coli BepA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Function of the beta-Barrel Assembly-Enhancing Protease BepA.

Shahrizal, M.Daimon, Y.Tanaka, Y.Hayashi, Y.Nakayama, S.Iwaki, S.Narita, S.I.Kamikubo, H.Akiyama, Y.Tsukazaki, T.

(2019) J. Mol. Biol. 431: 625-635

  • DOI: 10.1016/j.jmb.2018.11.024

  • PubMed Abstract: 
  • The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the ass ...

    The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the assembly and/or degradation of β-barrel membrane proteins. To elucidate the molecular mechanism underlying the dual functions of BepA, its full-length three-dimensional structure is needed. Here, we report the crystal structure of full-length BepA at 2.6-Å resolution. BepA possesses an N-terminal protease domain and a C-terminal tetratricopeptide repeat domain, which interact with each other. Domain cross-linking by structure-guided introduction of disulfide bonds did not affect the activities of BepA in vivo, suggesting that the function of this protein does not involve domain rearrangement. The full-length BepA structure is compatible with the previously proposed docking model of BAM complex and tetratricopeptide repeat domain of BepA.


    Organizational Affiliation

    Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan. Electronic address: ttsukazaki@mac.com.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan. Electronic address: yakiyama@infront.kyoto-u.ac.jp.,Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Faculty of Nutritional Sciences, University of Morioka, Iwate 020-0694, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-barrel assembly-enhancing protease
A, B, C, D, E, F
439Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bepA (yfgC)
EC: 3.4.-.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamACDE complex of the Bam β-barrel assembly machine
Find proteins for P66948 (Escherichia coli (strain K12))
Go to UniProtKB:  P66948
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D, E, F
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.598 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 85.844α = 113.61
b = 104.674β = 105.84
c = 104.971γ = 104.03
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP26119007
Japan Society for the Promotion of ScienceJapanJP26119007
Japan Society for the Promotion of ScienceJapanJP18H02405
Japan Society for the Promotion of ScienceJapanJP17H05669

Revision History 

  • Version 1.0: 2018-12-26
    Type: Initial release
  • Version 1.1: 2019-02-13
    Type: Data collection, Database references
  • Version 1.2: 2019-05-22
    Type: Data collection, Structure summary