6IQU

Crystal structure of Prc with PDZ domain deletion in complex with NlpI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Basis for the Differential Regulatory Roles of the PDZ Domain in C-Terminal Processing Proteases.

Chueh, C.K.Som, N.Ke, L.C.Ho, M.R.Reddy, M.Chang, C.I.

(2019) mBio 10

  • DOI: 10.1128/mBio.01129-19
  • Primary Citation of Related Structures:  
    6IQQ, 6IQS, 6IQR, 6IQU

  • PubMed Abstract: 
  • Carboxyl (C)-terminal processing proteases (CTPs) participate in protective and regulatory proteolysis in bacteria. The PDZ domain is central to the activity of CTPs but plays inherently different regulatory roles. For example, the PDZ domain inhibit ...

    Carboxyl (C)-terminal processing proteases (CTPs) participate in protective and regulatory proteolysis in bacteria. The PDZ domain is central to the activity of CTPs but plays inherently different regulatory roles. For example, the PDZ domain inhibits the activity of the signaling protease CtpB by blocking the active site but is required for the activation of Prc (or Tsp), a tail-specific protease that degrades SsrA-tagged proteins. Here, by structural and functional analyses, we show that in the unliganded resting state of Prc, the PDZ domain is docked inside the bowl-shaped scaffold without contacting the active site, which is kept in a default misaligned conformation. In Prc, a hydrophobic substrate sensor distinct from CtpB engages substrate binding to the PDZ domain and triggers a structural remodeling to align the active-site residues. Therefore, this work reveals the structural basis for understanding the contrasting roles of the PDZ domain in the regulation of CTPs. IMPORTANCE Prc, also known previously as Tsp, is the founding member of the carboxyl-terminal processing protease (CTP) family of PDZ domain-containing proteases that include CtpA and CtpB. The substrate-binding PDZ domain is responsible for regulating the protease activity of CTP proteases; however, the regulatory role of PDZ domain is stimulatory in Prc but inhibitory in CtpA/B. By determining a series of crystal structures of Prc in the unliganded resting state, this study presents the structural basis for PDZ-dependent activation of Prc, the results of which explain the contrasting roles of the PDZ domain in the regulation of the protease activity of CTPs.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoprotein NlpIA278Escherichia coli K-12Mutation(s): 0 
Gene Names: nlpIyhbMb3163JW3132
Find proteins for P0AFB1 (Escherichia coli (strain K12))
Explore P0AFB1 
Go to UniProtKB:  P0AFB1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tail-specific proteaseB596Escherichia coli K-12Mutation(s): 0 
Gene Names: prctspb1830JW1819
EC: 3.4.21.102
Find proteins for P23865 (Escherichia coli (strain K12))
Explore P23865 
Go to UniProtKB:  P23865
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.827α = 90
b = 151.082β = 90
c = 148.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references