6MPZ | pdb_00006mpz

Crystal structure of a double glycine motif protease from AMS/PCAT transporter in complex with the leader peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6MPZ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease.

Bobeica, S.C.Dong, S.Huo, L.Mazo, N.McLaughlin, M.I.H.Jimenez-Oses, G.Nair, S.K.van der Donk, W.A.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.42305
  • Primary Citation Related Structures: 
    6MPZ

  • PubMed Abstract: 

    The secretion of peptides and proteins is essential for survival and ecological adaptation of bacteria. Dual-functional ATP-binding cassette transporters export antimicrobial or quorum signaling peptides in Gram-positive bacteria. Their substrates contain a leader sequence that is excised by an N-terminal peptidase C39 domain at a double Gly motif. We characterized the protease domain (LahT150) of a transporter from a lanthipeptide biosynthetic operon in Lachnospiraceae and demonstrate that this protease can remove the leader peptide from a diverse set of peptides. The 2.0 Å resolution crystal structure of the protease domain in complex with a covalently bound leader peptide demonstrates the basis for substrate recognition across the entire class of such transporters. The structural data also provide a model for understanding the role of leader peptide recognition in the translocation cycle, and the function of degenerate, non-functional C39-like domains (CLD) in substrate recruitment in toxin exporters in Gram-negative bacteria.


  • Organizational Affiliation
    • Roger Adams Laboratory, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, United States.

Macromolecule Content 

  • Total Structure Weight: 72.86 kDa 
  • Atom Count: 5,010 
  • Modeled Residue Count: 619 
  • Deposited Residue Count: 644 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Double Glycine Motif Protease domain from AMS/PCAT Transporter
A, B, C, D
147Lachnospiraceae bacterium C6A11Mutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
peptide aldehyde inhibitor 1 based on the ProcA2.8 leader peptideE [auth M],
F [auth N],
G [auth O],
H [auth P]
14Prochlorococcus marinus str. MIT 9313Mutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
GLZ
Query on GLZ
E [auth M],
F [auth N],
G [auth O],
H [auth P]
L-PEPTIDE LINKINGC2 H5 N OGLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.268 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.888α = 90
b = 119.426β = 93.84
c = 76.522γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
AutoSolphasing
PHENIXmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM079038

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references, Refinement description, Structure summary