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 

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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 insertion of nascent PG material ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoprotein NlpIB [auth A],
A [auth B]		278Escherichia coli K-12Mutation(s): 0 
Gene Names: nlpI, yhbM, b3163, JW3132
UniProt
Find proteins for P0AFB1 (Escherichia coli (strain K12))
Explore P0AFB1 
Go to UniProtKB:  P0AFB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFB1
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tail-specific proteaseC, D682Escherichia coli K-12Mutation(s): 1 
Gene Names: prc, tsp, b1830, JW1819
EC: 3.4.21.102
UniProt
Find proteins for P23865 (Escherichia coli (strain K12))
Explore P23865 
Go to UniProtKB:  P23865
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23865
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALAE [auth F],
F [auth H]		6Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALAG [auth E]4Escherichia coli K-12Mutation(s): 0 
Protein Feature View
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
LEU-SER-ARG-SERH [auth G]4Escherichia 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

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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  (Full details and data files)

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