5WQL | pdb_00005wql

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

• PDB DOI: https://doi.org/10.2210/pdb5WQL/pdb

• Classification: PROTEIN BINDING/SIGNALING PROTEIN/HYDROLASE/PEPTIDE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Models: experimental

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

• PubMed: 29138488 
• DOI: https://doi.org/10.1038/s41467-017-01697-9
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.
Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA.
CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.
Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
Institute of Molecular Medicine, National Cheng Kung University, Tainan City, 70456, Taiwan.
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan. [e-mail].
Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 218.8 kDa 
• Atom Count: 15,704 
• Modeled Residue Count: 1,853 
• Deposited Residue Count: 1,940 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipoprotein NlpI	A [auth B], B [auth A]	278	Escherichia coli K-12	Mutation(s): 0  Gene Names: nlpI
UniProt
Find proteins for P0AFB1 (Escherichia coli (strain K12)) Explore P0AFB1  Go to UniProtKB:  P0AFB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail-specific protease	C, D	682	Escherichia coli K-12	Mutation(s): 1  Gene Names: prc EC: 3.4.21.102
UniProt
Find proteins for P23865 (Escherichia coli (strain K12)) Explore P23865  Go to UniProtKB:  P23865

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ALA-ALA-ALA-ALA	E [auth F], F [auth H]	6	Escherichia coli K-12	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ALA-ALA	G [auth E]	4	Escherichia coli K-12	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LEU-SER-ARG-SER	H [auth G]	4	Escherichia coli K-12	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.594	α = 90
b = 146.726	β = 90
c = 148.429	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
Coot	model building
HKL-2000	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-22 
Deposition Author(s): Su, M.Y., Chang, C.I.

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Funding Organization	Location	Grant Number
Academia Sinica	Taiwan	--

Revision History  

• Version 1.0: 2017-11-22
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description