6AIT

Crystal structure of E. coli BepA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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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
  • Primary Citation of Related Structures:  
    6AIT

  • 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 assembly and/or degradation of β-barrel membrane proteins ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-barrel assembly-enhancing protease
A, B, C, D, E, F
A, B, C, D, E, F
439Escherichia coli K-12Mutation(s): 0 
Gene Names: bepA, yfgC, b2494, JW2479
EC: 3.4
Membrane Entity: Yes 
UniProt
Find proteins for P66948 (Escherichia coli (strain K12))
Explore P66948 
Go to UniProtKB:  P66948
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP66948
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • 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
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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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  (Full details and data files)

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