7W71

Crystal structure of the PDZ-C domain of E. coli RseP in complex with 12C7 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of sigma-E protease RsePA [auth B],
B [auth A]
93Escherichia coliMutation(s): 0 
Gene Names: rsePecfEyaeLb0176JW0171
EC: 3.4.24
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of FabC [auth H],
E [auth I]
218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of FabD [auth L],
F [auth M]
214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.099α = 90
b = 77.271β = 90
c = 283.633γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary