8D19

Human LanCL1 bound to GSH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The mechanism of thia-Michael addition catalyzed by LanC enzymes.

Ongpipattanakul, C.Liu, S.Luo, Y.Nair, S.K.van der Donk, W.A.

(2023) Proc Natl Acad Sci U S A 120: e2217523120-e2217523120

  • DOI: https://doi.org/10.1073/pnas.2217523120
  • Primary Citation of Related Structures:  
    8CZK, 8CZL, 8D0V, 8D19

  • PubMed Abstract: 

    In both eukarya and bacteria, the addition of Cys to dehydroalanine (Dha) and dehydrobutyrine (Dhb) occurs in various biological processes. In bacteria, intramolecular thia-Michael addition catalyzed by lanthipeptide cyclases (LanC) proteins or protein domains gives rise to a class of natural products called lanthipeptides. In eukarya, dehydroamino acids in signaling proteins are introduced by effector proteins produced by pathogens like Salmonella to dysregulate host defense mechanisms. A eukaryotic LanC-like (LanCL) enzyme catalyzes the addition of Cys in glutathione to Dha/Dhb to protect the cellular proteome from unwanted chemical and biological activity. To date, the mechanism of the enzyme-catalyzed thia-Michael addition has remained elusive. We report here the crystal structures of the human LanCL1 enzyme complexed with different ligands, including the product of thia-Michael addition of glutathione to a Dhb-containing peptide that represents the activation loop of Erk. The structures show that a zinc ion activates the Cys thiolate for nucleophilic attack and that a conserved His is poised to protonate the enolate intermediate to achieve a net anti- addition. A second His hydrogen bonds to the carbonyl oxygen of the former Dhb and may stabilize the negative charge that builds up on this oxygen atom in the enolate intermediate. Surprisingly, the latter His is not conserved in orthologous enzymes that catalyze thia-Michael addition to Dha/Dhb. Eukaryotic LanCLs contain a His, whereas bacterial stand-alone LanCs have a Tyr residue, and LanM enzymes that have LanC-like domains have a Lys, Asn, or His residue. Mutational and binding studies support the importance of these residues for catalysis.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase LANCL1
A, B
419Homo sapiensMutation(s): 0 
Gene Names: LANCL1GPR69A
EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for O43813 (Homo sapiens)
Explore O43813 
Go to UniProtKB:  O43813
PHAROS:  O43813
GTEx:  ENSG00000115365 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43813
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.505α = 90
b = 121.134β = 90
c = 142.895γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AutoProcessdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description