3E73 | pdb_00003e73

Crystal Structure of Human LanCL1 complexed with GSH

• PDB DOI: https://doi.org/10.2210/pdb3E73/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-08-17 Released: 2009-06-30 
• Deposition Author(s): Zhang, W., Zhu, G., Li, X., Rao, Z., Zhang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structure of human lanthionine synthetase C-like protein 1 and its interaction with Eps8 and glutathione

Zhang, W., Wang, L., Liu, Y., Xu, J., Zhu, G., Cang, H., Li, X., Bartlam, M., Hensley, K., Li, G., Rao, Z., Zhang, X.C.

(2009) Genes Dev 23: 1387-1392

• PubMed: 19528316 
• DOI: https://doi.org/10.1101/gad.1789209
• Primary Citation of Related Structures:  
  3E6U, 3E73


• PubMed Abstract: 
  

  Eukaryotic lanthionine synthetase C-like protein 1 (LanCL1) is homologous to prokaryotic lanthionine cyclases, yet its biochemical functions remain elusive. We report the crystal structures of human LanCL1, both free of and complexed with glutathione, revealing glutathione binding to a zinc ion at the putative active site formed by conserved GxxG motifs. We also demonstrate by in vitro affinity analysis that LanCL1 binds specifically to the SH3 domain of a signaling protein, Eps8. Importantly, expression of LanCL1 mutants defective in Eps8 interaction inhibits nerve growth factor (NGF)-induced neurite outgrowth, providing evidence for the biological significance of this novel interaction in cellular signaling and differentiation.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.51 kDa 
• Atom Count: 6,553 
• Modelled Residue Count: 804 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LanC-like protein 1	A, B	411	Homo sapiens	Mutation(s): 0  Gene Names: LANCL1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	D [auth A], F [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.1	α = 90
b = 194.101	β = 90
c = 243.554	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-30 
Deposition Author(s): Zhang, W., Zhu, G., Li, X., Rao, Z., Zhang, C.

Revision History  

• Version 1.0: 2009-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description