7W6Z

Crystal structure of Kangiella koreensis RseP orthologue in complex with batimastat in space group P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc metalloprotease456Kangiella koreensis DSM 16069Mutation(s): 0 
Gene Names: Kkor_1905
EC: 3.4.24
Membrane Entity: Yes 
UniProt
Find proteins for C7R5Z1 (Kangiella koreensis (strain DSM 16069 / KCTC 12182 / SW-125))
Explore C7R5Z1 
Go to UniProtKB:  C7R5Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7R5Z1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BAT
Query on BAT

Download Ideal Coordinates CCD File 
C [auth A]4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE
C23 H31 N3 O4 S2
XFILPEOLDIKJHX-QYZOEREBSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.267 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.27α = 90
b = 40.8β = 91.613
c = 160.24γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing

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: 2024-11-06
    Changes: Data collection, Structure summary