Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 294.45 kDa 
• Atom Count: 19732 
• Residue Count: 2483 
• Unique protein chains: 1

6AIT

Crystal structure of E. coli BepA

• DOI: 10.2210/pdb6AIT/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-24 Released: 2018-12-26 
• Deposition Author(s): Umar, M.S.M., Tanaka, Y., Kamikubo, H., Tsukazaki, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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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 

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

• PubMed: 30521812 
• 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. 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.

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Organizational Affiliation: 

Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-barrel assembly-enhancing protease	A, B, C, D, E, F	439	Escherichia coli K-12	Mutation(s): 0  Gene Names: bepA, yfgC, b2494, JW2479 EC: 3.4
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Omp85-TpsB Outer Membrane Transporter Superfamily	Protein:  BepA (YfgC) BAM assembly-enhancing protease
Find proteins for P66948 (Escherichia coli (strain K12)) Explore P66948  Go to UniProtKB:  P66948

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	A, B, C, D, E, F	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	A, B, C, D, E, F	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 85.844	α = 113.61
b = 104.674	β = 105.84
c = 104.971	γ = 104.03

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-24 
• Released Date: 2018-12-26 
Deposition Author(s): Umar, M.S.M., Tanaka, Y., Kamikubo, H., Tsukazaki, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	JP26119007
Japan Society for the Promotion of Science	Japan	JP26119007
Japan Society for the Promotion of Science	Japan	JP18H02405
Japan Society for the Promotion of Science	Japan	JP17H05669

Revision History 

• 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