6WQ1 | pdb_00006wq1

Eukaryotic LanCL2 protein

• PDB DOI: https://doi.org/10.2210/pdb6WQ1/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-28 Released: 2021-05-05 
• Deposition Author(s): Nair, S.K., Garg, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

LanCLs add glutathione to dehydroamino acids generated at phosphorylated sites in the proteome.

Lai, K.Y., Galan, S.R.G., Zeng, Y., Zhou, T.H., He, C., Raj, R., Riedl, J., Liu, S., Chooi, K.P., Garg, N., Zeng, M., Jones, L.H., Hutchings, G.J., Mohammed, S., Nair, S.K., Chen, J., Davis, B.G., van der Donk, W.A.

(2021) Cell 184: 2680-2695.e26

• PubMed: 33932340 
• DOI: https://doi.org/10.1016/j.cell.2021.04.001
• Primary Citation Related Structures: 
  6WQ1


• PubMed Abstract: 
  

  Enzyme-mediated damage repair or mitigation, while common for nucleic acids, is rare for proteins. Examples of protein damage are elimination of phosphorylated Ser/Thr to dehydroalanine/dehydrobutyrine (Dha/Dhb) in pathogenesis and aging. Bacterial LanC enzymes use Dha/Dhb to form carbon-sulfur linkages in antimicrobial peptides, but the functions of eukaryotic LanC-like (LanCL) counterparts are unknown. We show that LanCLs catalyze the addition of glutathione to Dha/Dhb in proteins, driving irreversible C-glutathionylation. Chemo-enzymatic methods were developed to site-selectively incorporate Dha/Dhb at phospho-regulated sites in kinases. In human MAPK-MEK1, such "elimination damage" generated aberrantly activated kinases, which were deactivated by LanCL-mediated C-glutathionylation. Surveys of endogenous proteins bearing damage from elimination (the eliminylome) also suggest it is a source of electrophilic reactivity. LanCLs thus remove these reactive electrophiles and their potentially dysregulatory effects from the proteome. As knockout of LanCL in mice can result in premature death, repair of this kind of protein damage appears important physiologically.

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Organizational Affiliation: 
• Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK.
Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0FA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK.
Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Dana-Farber Cancer Institute, 360 Longwood Avenue, Boston, MA 02115, USA.
UK Catalysis Hub, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxford OX11 0FA, UK; Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK.
Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK.
Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: [e-mail].
Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield, Oxford OX1 3TA, UK; The Rosalind Franklin Institute, Oxfordshire OX11 0FA, UK. Electronic address: [e-mail].
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 203.95 kDa 
• Atom Count: 13,475 
• Modeled Residue Count: 1,583 
• Deposited Residue Count: 1,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LanC-like protein 2	A, B, C, D	450	Homo sapiens	Mutation(s): 0  Gene Names: LANCL2, GPR69B, TASP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS86 (Homo sapiens) Explore Q9NS86  Go to UniProtKB:  Q9NS86
PHAROS:  Q9NS86 GTEx:  ENSG00000132434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.415	α = 90
b = 108.012	β = 91.26
c = 152.013	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Nair, S.K., Garg, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description