5WQL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

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
  • Primary Citation of Related Structures:  
    5WQL

  • 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 Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan. chungi@gate.sinica.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoprotein NlpIAB278Escherichia coli K-12Mutation(s): 0 
Gene Names: nlpIyhbMb3163JW3132
Find proteins for P0AFB1 (Escherichia coli (strain K12))
Explore P0AFB1 
Go to UniProtKB:  P0AFB1
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tail-specific proteaseCD682Escherichia coli K-12Mutation(s): 1 
Gene Names: prctspb1830JW1819
EC: 3.4.21.102
Find proteins for P23865 (Escherichia coli (strain K12))
Explore P23865 
Go to UniProtKB:  P23865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALAFH6Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALAE4Escherichia coli K-12Mutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
LEU-SER-ARG-SERG4Escherichia coli K-12Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.594α = 90
b = 146.726β = 90
c = 148.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report



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
    Changes: Database references