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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.262 (Depositor), 0.258 (DCC)
R-Value Work:
0.231 (Depositor), 0.228 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/gad.1789209
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43813
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	D [auth A], F [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.262 (Depositor), 0.258 (DCC)
R-Value Work: 0.231 (Depositor), 0.228 (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

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Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Revision History (Full details and data files)

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