7W6X | pdb_00007w6x

Crystal structure of E. coli RseP in complex with batimastat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.305 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.249 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7W6X

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP.

Imaizumi, Y.Takanuki, K.Miyake, T.Takemoto, M.Hirata, K.Hirose, M.Oi, R.Kobayashi, T.Miyoshi, K.Aruga, R.Yokoyama, T.Katagiri, S.Matsuura, H.Iwasaki, K.Kato, T.Kaneko, M.K.Kato, Y.Tajiri, M.Akashi, S.Nureki, O.Hizukuri, Y.Akiyama, Y.Nogi, T.

(2022) Sci Adv 8: eabp9011-eabp9011

  • DOI: https://doi.org/10.1126/sciadv.abp9011
  • Primary Citation Related Structures: 
    7W6X, 7W6Y, 7W6Z, 7W70, 7W71

  • PubMed Abstract: 

    Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including Escherichia coli RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments.


  • Organizational Affiliation
    • Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Macromolecule Content 

  • Total Structure Weight: 50.71 kDa 
  • Atom Count: 3,478 
  • Modeled Residue Count: 447 
  • Deposited Residue Count: 458 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Regulator of sigma-E protease RseP458Escherichia coli K-12Mutation(s): 0 
Gene Names: rsePecfEyaeLb0176JW0171
EC: 3.4.24
Membrane Entity: Yes 
UniProt
Find proteins for P0AEH1 (Escherichia coli (strain K12))
Explore P0AEH1 
Go to UniProtKB:  P0AEH1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEH1
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A
L-PEPTIDE LINKINGC6 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.305 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.34α = 68.167
b = 56.12β = 74.591
c = 69.67γ = 69.346
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H03170
Japan Society for the Promotion of Science (JSPS)Japan26291016
Japan Society for the Promotion of Science (JSPS)Japan22370039
Japan Society for the Promotion of Science (JSPS)Japan19687004

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary