5WQL

Structure of a PDZ-protease bound to a substrate-binding adaptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural basis of adaptor-mediated protein degradation by the tail-specific PDZ-protease Prc

Su, M.Y., Som, N., Wu, C.Y., Su, S.C., Kuo, Y.T., Ke, L.C., Ho, M.R., Tzeng, S.R., Teng, C.H., Mengin-Lecreulx, D., Reddy, M., Chang, C.I.

(2017) Nat Commun 8: 1516-1516

  • DOI: 10.1038/s41467-017-01697-9

  • PubMed Abstract: 

    • Peptidoglycan (PG) is a highly cross-linked, protective mesh-like sacculus that surrounds the bacterial cytoplasmic membrane. Expansion of PG is tightly coupled to growth of a bacterial cell and requires hydrolases to cleave the cross-links for inser ...

    Peptidoglycan (PG) is a highly cross-linked, protective mesh-like sacculus that surrounds the bacterial cytoplasmic membrane. Expansion of PG is tightly coupled to growth of a bacterial cell and requires hydrolases to cleave the cross-links for insertion of nascent PG material. In Escherichia coli, a proteolytic system comprising the periplasmic PDZ-protease Prc and the lipoprotein adaptor NlpI contributes to PG enlargement by regulating cellular levels of MepS, a cross-link-specific hydrolase. Here, we demonstrate how NlpI binds Prc to facilitate the degradation of its substrate MepS by structural and mutational analyses. An NlpI homodimer binds two molecules of Prc and forms three-sided MepS-docking cradles using its tetratricopeptide repeats. Prc forms a monomeric bowl-shaped structure with a lid-like PDZ domain connected by a substrate-sensing hinge that recognizes the bound C terminus of the substrate. In summary, our study reveals mechanistic details of protein degradation by the PDZ-protease Prc bound to its cognate adaptor protein.

    Organizational Affiliation: 

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein NlpI
B, A
278Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nlpI (yhbM)
Find proteins for P0AFB1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFB1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tail-specific protease
C, D
682Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: prc (tsp)
EC: 3.4.21.102
Find proteins for P23865 (Escherichia coli (strain K12))
Go to UniProtKB:  P23865
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA-ALA-ALA
F, H
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ALA-ALA
E
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
LEU-SER-ARG-SER
G
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 120.594α = 90.00
b = 146.726β = 90.00
c = 148.429γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data processing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-11-27 
  • Released Date: 2017-11-22 
  • Deposition Author(s): Su, M.Y., Chang, C.I.
Funding OrganizationLocationGrant Number
Academia SinicaTaiwan--

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references