Integral membrane domain of autotransporter Hbp

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A novel intein-like autoproteolytic mechanism in autotransporter proteins.

Tajima, N.Kawai, F.Park, S.Y.Tame, J.R.

(2010) J Mol Biol 402: 645-656

  • DOI: https://doi.org/10.1016/j.jmb.2010.06.068
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Many virulence factors secreted by pathogenic Gram-negative bacteria are found to be members of the autotransporter protein family. These proteins share a common mechanism by which they exit the periplasm, involving the formation of a 12-stranded β-barrel domain in the outer membrane. The role of this barrel in the secretion of the N-terminal passenger domain is controversial, and no model currently explains satisfactorily the entire body of experimental data. After secretion, some autotransporter barrels autoproteolytically cleave away the passenger, and one crystal structure is known for a barrel of this type in the postcleavage state. Hbp is an autotransporter of the self-cleaving type, which cuts the polypeptide between two absolutely conserved asparagine residues buried within the barrel lumen. Mutation of the first asparagine residue to isosteric aspartic acid prevents proteolysis. Here we present the crystal structure of a truncated Hbp mutant carrying the C-terminal residues of the passenger domain attached to the barrel. This model mimics the state of the protein immediately prior to separation of the passenger and barrel domains, and shows the role of residues in the so-called "linker" between the passenger and β domains. This high-resolution membrane protein crystal structure also reveals the sites of many water molecules within the barrel. The cleavage mechanism shows similarities to those of inteins and some viral proteins, but with a novel means of promoting nucleophilic attack.

  • Organizational Affiliation

    Yokohama City University, Suehiro 1-7-29, Tsurumi, Yokohama 230-0045, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin-binding protease hbp autotransporter
A, B
308Escherichia coliMutation(s): 1 
Gene Names: hbp
EC: 3.4.21
Membrane Entity: Yes 
Find proteins for O88093 (Escherichia coli)
Explore O88093 
Go to UniProtKB:  O88093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88093
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.011α = 90
b = 68.893β = 117.75
c = 78.378γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-01-18
    Changes: Database references
  • Version 1.3: 2021-11-10
    Changes: Database references