7UBZ | pdb_00007ubz

Chymotrypsin digested toxin/immunity complex for a T6SS lipase effector from E. cloacae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Advanced glycation end-product crosslinking activates a type VI secretion system phospholipase effector protein.

Jensen, S.J.Cuthbert, B.J.Garza-Sanchez, F.Helou, C.C.de Miranda, R.Goulding, C.W.Hayes, C.S.

(2024) Nat Commun 15: 8804-8804

  • DOI: https://doi.org/10.1038/s41467-024-53075-x
  • Primary Citation of Related Structures:  
    7UBZ, 9CYS

  • PubMed Abstract: 

    Advanced glycation end-products (AGE) are a pervasive form of protein damage implicated in the pathogenesis of neurodegenerative disease, atherosclerosis and diabetes mellitus. Glycation is typically mediated by reactive dicarbonyl compounds that accumulate in all cells as toxic byproducts of glucose metabolism. Here, we show that AGE crosslinking is harnessed to activate an antibacterial phospholipase effector protein deployed by the type VI secretion system of Enterobacter cloacae. Endogenous methylglyoxal reacts with a specific arginine-lysine pair to tether the N- and C-terminal α-helices of the phospholipase domain. Substitutions at these positions abrogate both crosslinking and toxic phospholipase activity, but in vitro enzyme function can be restored with an engineered disulfide that covalently links the N- and C-termini. Thus, AGE crosslinking serves as a bona fide post-translation modification to stabilize phospholipase structure. Given the ubiquity of methylglyoxal in prokaryotic and eukaryotic cells, these findings suggest that glycation may be exploited more generally to stabilize other proteins. This alternative strategy to fortify tertiary structure could be particularly advantageous in the cytoplasm, where redox potentials preclude disulfide bond formation.


  • Organizational Affiliation

    Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, 93106, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ankyrin repeat domain-containing proteinA,
B [auth C]
230Enterobacter cloacaeMutation(s): 0 
Gene Names: I6L61_16350
UniProt
Find proteins for A0A0H3CKN4 (Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCTC 10005 / WDCM 00083 / NCDC 279-56))
Explore A0A0H3CKN4 
Go to UniProtKB:  A0A0H3CKN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3CKN4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
T6SS lipase effectorC [auth B],
D
313Enterobacter cloacaeMutation(s): 0 
Gene Names: NCTC10005_04014
UniProt
Find proteins for A0A0M7ENE2 (Enterobacter cloacae)
Explore A0A0M7ENE2 
Go to UniProtKB:  A0A0M7ENE2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M7ENE2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download Ideal Coordinates CCD File 
H [auth C]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth C]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth C],
J [auth B],
L [auth B],
M [auth B],
O [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MIE (Subject of Investigation/LOI)
Query on MIE

Download Ideal Coordinates CCD File 
K [auth B],
N [auth D]
methylglyoxal
C3 H4 O2
AIJULSRZWUXGPQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.172α = 90
b = 120.493β = 90
c = 122.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesGM117930

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary
  • Version 1.3: 2024-11-13
    Changes: Database references