8XUD

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 
    0.272 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structural basis for recruitment of peptidoglycan endopeptidase MepS by lipoprotein NlpI.

Wang, S.Huang, C.H.Lin, T.S.Yeh, Y.Q.Fan, Y.S.Wang, S.W.Tseng, H.C.Huang, S.J.Chang, Y.Y.Jeng, U.S.Chang, C.I.Tzeng, S.R.

(2024) Nat Commun 15: 5461-5461

  • DOI: https://doi.org/10.1038/s41467-024-49552-y
  • Primary Citation of Related Structures:  
    8XUD, 8XUP

  • PubMed Abstract: 

    Peptidoglycan (PG) sacculi surround the cytoplasmic membrane, maintaining cell integrity by withstanding internal turgor pressure. During cell growth, PG endopeptidases cleave the crosslinks of the fully closed sacculi, allowing for the incorporation of new glycan strands and expansion of the peptidoglycan mesh. Outer-membrane-anchored NlpI associates with hydrolases and synthases near PG synthesis complexes, facilitating spatially close PG hydrolysis. Here, we present the structure of adaptor NlpI in complex with the endopeptidase MepS, revealing atomic details of how NlpI recruits multiple MepS molecules and subsequently influences PG expansion. NlpI binding elicits a disorder-to-order transition in the intrinsically disordered N-terminal of MepS, concomitantly promoting the dimerization of monomeric MepS. This results in the alignment of two asymmetric MepS dimers respectively located on the two opposite sides of the dimerization interface of NlpI, thus enhancing MepS activity in PG hydrolysis. Notably, the protein level of MepS is primarily modulated by the tail-specific protease Prc, which is known to interact with NlpI. The structure of the Prc-NlpI-MepS complex demonstrates that NlpI brings together MepS and Prc, leading to the efficient MepS degradation by Prc. Collectively, our results provide structural insights into the NlpI-enabled avidity effect of cellular endopeptidases and NlpI-directed MepS degradation by Prc.


  • Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein NlpI
A, B
297Escherichia coli K-12Mutation(s): 0 
Gene Names: nlpIyhbMb3163JW3132
UniProt
Find proteins for P0AFB1 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AFB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFB1
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tail-specific protease
C, D
688Escherichia coli K-12Mutation(s): 2 
Gene Names: prctspb1830JW1819
EC: 3.4.21.102
UniProt
Find proteins for P23865 (Escherichia coli (strain K12))
Explore P23865 
Go to UniProtKB:  P23865
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23865
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidaseE [auth I],
F [auth J],
G [auth K],
H [auth L]
168Escherichia coli K-12Mutation(s): 0 
Gene Names: mepSspryeiVb2175JW2163
EC: 3.4 (PDB Primary Data), 3.4.17.13 (PDB Primary Data)
UniProt
Find proteins for P0AFV4 (Escherichia coli (strain K12))
Explore P0AFV4 
Go to UniProtKB:  P0AFV4
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UniProt GroupP0AFV4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Substrate peptideI [auth M]8Escherichia coli K-12Mutation(s): 0 
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Substrate peptideJ [auth N]9Escherichia coli K-12Mutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
K [auth I]
L [auth I]
M [auth I]
N [auth I]
O [auth J]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 230.41α = 90
b = 230.41β = 90
c = 182.905γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references, Structure summary